A Super Prototype is a testbed version of some piece of technology — like a Humongous Mecha, Space Fighter, or Killer Robot — that is, for some reason, superior to the mass-produced version. A super prototype will have better weapons, stronger armor, and higher-quality speakers than the units rolling off the assembly line. Even when there isn't very many of whatever device was designed in the first place, the prototype model is almost always the most powerful, or has at least some advantage over the other models.
A question that often comes up is why the super prototype is so, well, super compared to the production model. The typical reason given is that the production model is far cheaper or easier to make in large numbers. Sometimes, the technology that makes the device so much more powerful is Lost Technology (although one wonders why a prototype of a future possible design would include tech the mass-produced versions would never be capable of including), and thus not easily replicated. Or the technology in the prototype is difficult to use, thus requiring an Ace Pilot to operate, while the later models are less powerful but stable enough for normal soldiers to use. Mass-production models were likely made (in the grand tradition of military equipment) by the lowest bidder, who cut corners wherever possible. But mostly, it just lets The Hero be that much more awesome.
In Real Life, a prototype is simply the first unit of a model to be built, usually made in order to do real-world tests of the design and correct any flaws before mass production begins. As such, you want your test unit to be as similar to your production unit as possible, so prototypes are frequently indistinguishable from standard models. note Additionally, in Real Life prototypes of armoured vehicles (and this would apply to armour-clad Gundams and such as well) are typically made from "soft" (non-armour grade) steel to simplify building and modification, so their life on the battlefield would've been rather short
However, a real-world concept that more closely resembles the super prototype is the experimental unit, which is intended to test out new technology without ever being meant for mass production at all. As cost-effectiveness is less important, experimental units frequently do have superior performance to eventual mass production models. Military test pilots refer to this as "pushing the envelope" - the upper edge is height, the left edge is speed. Visualize this as the kind of envelope you mail somebody and you realize that particular area is where the postage gets canceled. This distinction is rarely made in fiction, however. note As an aside, often times in electronics, companies will ship out the most powerful unit first to show what the next gen is capable of. All subsequent models are usually lesser versions of that first release (which are usually production units that failed and are either ran at lower performance or have parts chopped off), though occasionally when technology improves, they might make a revision to the design to make it even better.
May be the result of a Black Box; the "super" parts of the prototype are unreplicable. A specific instance of Older Is Better: the prototype came first, so it is better than all that came after it. The Opposite Trope is the Flawed Prototype and Superior Successor. A closely related trope is the Ace Custom. See also Reed Richards Is Useless and Bigger Stick.
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Anime and Manga
The Gundam metaseries makes extensive use this trope. Pretty much any mecha with "Gundam" in its name will be either a Super Prototype, an Ace Custom, or both. Which justified in-universe with reason of cost-effectiveness, the prototype usually carries better reactor, alloy and trinkets which later changed to cheaper and inferior version or removed from the mass production unit so they can produce a lot more with same amount of budget and resources. Few exceptions are:
Mobile Suit Victory Gundamtwist it. While the titular Victory Gundam is superior to its simplified sister model Gun EZ, the actual mass production model is identical to the prototype. The Victory 2 was meant to be a limited-production model, but the other suits were destroyed prior to being fielded, leaving Uso's V2 as a unique unit.
The Astray line is an odd case. The colored Frames (Red, Blue, Gold, Green and Mirage) were all prototypes, but weren't anything incredible. Only by the wonders of Ace Custom that they became superior to the later mass produced Astray units. And even then, the Astray could take on the prototypes, as the Red Frame was once easily taken down by a simple Astray (granted one piloted by Coordinator.)
However, Gundam SEED does play the trope straight with the Moebius mobile armor. The Moebius Zero prototype sports four detachable and independently maneuverable gunbarrels in a precursor to the DRAGOON system later used to great effect by certain Bigger Stick mecha like the Providence; the production model Moebius lacks these, using only the forward-fixed central cannon. This is justified in that only a select few OMNI pilots had the spatial awareness and piloting skills required to use the detachable gunbarrels anything like effectively, and of those pilots only Ace Pilot Mu la Flaga survived the Battle of Endymion prior to the start of the anime, so paring down the design was an unfortunate necessity.
It's also noteworthy that in Mobile Suit Zeta Gundam this trope becomes the shtick of Paptimus Scirocco. Over the course of the series he cranks out one-shot, scratch-built mobile suits at an astonishing rate. The Messala, Pallas Athena, Bolinoak Samaan and The-O are all unique Scirocco designs, while the Gabthley and Hambrabi are limited production models designed by Scirocco for the Federation's use and only 2-4 of each were ever made. In general, Scirocco's godlike ability to crank out butt-kicking mobile suits is used as a catch-all explanation for all Titans Super Prototype suits that aren't the Psyco Gundam.
And the Gundam Mk-II actually inverts this - even though it was a Super Prototype and, for awhile, could one-up the Titans' Hi-Zack units, there was nothing special about it outside of its special lighter frame system and it's easily outclassed early on.
The Tallgeese in Gundam Wing was the precursor to all mobile suits in that universe. It's so powerful it can hold its own against the first generation of Gundams in that series. It did have one glaring design flaw: it was so powerful that it killed its own pilots. The Leos that were based on its design are far weaker but also safer for people to pilot.
Tough in general, the super prototype remain superior only to the same generation series as technological race is a strong theme in gundam series making the next generation units usually better than the previous generation super prototype.
The 08th MS Team actually averts this. The series is known for instead of making a traditional Gundam series about a boy Falling into the Cockpit and getting involved in the current war, and instead focuses on the everyday soldiers in the One Year War. Because of this, most pilots in the series don't have brand-new prototype Mobile Suits. Instead they have things like the RX-79(G) Gundam Ground Type, which is merely spare parts from the RX-78 Gundam program made into a mass-produced Gundam designed for ground combat. There's also the Gundam Ez8, which is an RX-79(G) rebuilt with field-fabricated parts due to lack of spares. One poor one even had its destroyed head unit replaced with a GM's.
Chi and Freya from Chobits were two of the first persocoms ever built, yet their capabilities exceed any that were built after them.
Super Dimension Fortress Macross usually averts this, with the production models being built up from the prototype's capabilities. Even Macross Zero only uses Flawed Prototype in the form of the VF-0 Phoenix: despite having flight performance head-and-shoulders above conventional jet aircraft and even limited capability for underwater operation, it's a maintenance-hog and the war's outbreak meant that the engineers couldn't wait until the intended space-capable reactor engines were completed so they simply slapped on the strongest airbreathing jet engine they could get their hands on and crossed their fingers.
The majority of Macross Plus consists of a contest between two super prototypes (YF-19 and YF-21) competing to be the new mass production model; they eventually choose the YF-19 after the YF-21's Unusual User Interface proves to be a little unsafe if the pilot gets distracted during flight; the destruction of the YF-21 prototype doesn't help either. This is actually a realistic portrayal of the prototyping system; similar contests have actually occurred in real life.
The VF-25 the good guys use in Macross Frontier also has superior performance to the military standard-issue VF-171 along with a redesigned Armored Pack that won't lock the Valkyrie into battroid mode; while the civilian protagonist recognizes it on sight, it's confirmed as still undergoing official performance evaluations.
In a way, Madara Uchiha and Hashirama Senju are this compared to most ninja in the Naruto universe. Due to living in an age of constant warfare, their abilities were brought to such a zenith that, as Kabuto Yakushi described, many people thought it was a fairy tale, specifically Hashirama. We've seen characters like Yamato, Danzo, even Tobi with Mokuton which doesn't remotely compare to Hashirama, and Sasuke and Itachi both achieved the same Mangekyo Sharingan powers as Madara, specifically the Power Armor, Made Of DiamondSusnao'o, but Madara's Susano'o is on such a far higher scale than both combined, Tsunade, one of the current Kages and one of the most powerful shinobi of her era, wondered how the fuck did her grandfather even fight Madara?
And the Biju themselves, even Kurama are far weaker than the original Biju, the Shinju or 'God Tree' which is in itself the Ten-Tails.
One Piece has the World Government-developed Pacifistas. The original, created by rebuildingBad Ass Bartholemew Kuma into a Hollywood Cyborg, is able to make short work of some later models, though this is mostly because Kuma had Devil Fruit powers that apparently couldn't be transferred to the others or technologically duplicated. It is stated that more powerful models have been created over the Time Skip, though it has not yet been shown how well Kuma would stack up against them.
The police protagonists on Patlabor had three prototype AV-98 Ingram mechs. One episode focused on the introduction of a mass-produced line of Ingrams, subverting the trope a bit in that the prototypes weren't exceptionally good so much as the mass-produced ones were exceptionally shoddy. Also, other kinds of mass-produced police and military mechs are shown to be close in quality to the Ingrams.
The first film has the Type Zero which was supposed to be an advanced replacement for the AV-98. It proved to be a fearsome opponent in melee combat against other labors and when it was overtaken by the Babel virus, it completely mopped the floor with Ohta's Ingram and Noa barely managed to subdue it. Seeing as the Type Zero wasn't seen in the subsequent films, it can be assumed that the design was abandoned.
One character from Lyrical Nanoha, Subaru Nakajima is a self-admitted homage to Super Robot Wars. It turns out that she is the prototype to the Number cyborgs, stronger than the rest of them, and so is her sister Ginga. The special moves "borrowed" from such Super Robots like Gear Fighter Dendoh, GaoGaiGar, Combattler V and more make this homage especially apparent.
Fate Testarossa is another super prototype in a way — she was the very first successful Artificial Human created by an illegal cloning project run by the master of the Numbers, Jail Scaglietti. She bears the project's original name, and is the prototype that Jail used to create all the other Artificial Mages of the setting. However, to her mother, Fate is a Flawed Prototype because she was meant to be a clone of her dead daughter Alicia, but ended up gaining quirks of her own which royally pissed off mommy dearest.
Simultaneously subverted and played straight in Sentou Mecha Xabungle. The titular mecha (referred to as such by the regularly no-fourth-wall characters) is both a production model — they get two of them, unheard of in a mecha show up to that point — and a prototype in the sense that a) no prior Walker Machine is built specifically for combat (hence the series name — Combat Mecha) and b) it incorporates a number of features that imply it to be a space machine. The Walker Gallier in the second half of the show is a textbook example (and even has a production model of sorts in the Brackary). It's famously "Super" enough to catch and throw a falling ICBM (albeit a museum copy, but still).
Ram-Dass in Soukou No Strain is an illegally made mecha where the Union only condones standard issue. Because Sara saved them in it, it's explained away as a "prototype" to anyone that asks. Her brother's Gloire, on the other hand, is an Ace Custom.
Gimi: Anyway, aren't Grappals supposed to be superior to Gurren Lagann? There's something wrong with a prototype being stronger.
The trick here wasn't intentionally dumbing down the mass-produced version but rather the designers being ignorant of one crucial fact: the Gurren Lagann, like all Ganmen, is an Empathic Weapon. Simply copying the machinery won't help if they don't know what makes it tick. Once this fact is discovered, they quick-fix the situation with the addition of Spiral weaponry but they're still nowhere near enough Ganmen territory.
As seen in the movies, if your will is high enough, even the mass production models can grow into galaxy sized bots, a la "Tengen Toppa Grappal/Gulaparl" and fire planet system-sized shotgun rounds.
Code Geass features several super prototypes, progressing in power with the times. Supplementary materials explain the backstory of KMF development, where they were literally putting pieces together just to see how it worked; the best subversion of this trope is the Ganymede, the very first KMF to be built. It has no internal power source, only batteries; no weapons, no closed cockpit and insufficient motive power to do anything other than harmlessly cruising. It can make the world's biggest pizza, though.
Another subversion is the Gawain; when Lelouch jacked it, it was an Awesome, but Impractical KMF. It could fly, but a flaw in the hadron cannons left the beam unfocused, causing it to spew energy in a wide arc which could just as easily hit friend as well as foe. That problem was fixed, making the beams extremely deadly, but it was still outmatched in close combat. Its mass-production version, the Gareth, had the cannons moved it its hands.
To a smaller extent, the Vincent: the Vincent Ward final version scraps the needle blazer weapon to ease production. Of course, no one can forget the Vincent's own Super Prototype, the Lancelot: the world's first seventh-generation KMF, later upgraded into the one-of-a-kind ninth-generation unholy terror known as the Lancelot Albion.
One the opposite side of the coin, Guren Nishiki gets two successors: the limited-production Gekka and the mass-production Akatsuki (as well as Tohdoh's Zangetsu). Neither can hold a candle to the original, especially after it receives its own ninth-gen upgrade into the Guren SEITEN.
That said, this may be due to the pilot, but no direct comparison is made between the Guren's abilities and any of it's MP derivatives. Also, the Prototype Radiation Arm used by the Guren Nishiki after it's original Radiation Arm is destroyed seems to be both weaker, and not as well built, but this is also difficult to compare.
Appears as an Unbuilt Trope in Mazinger Z, the archetypal Super Robot series. Mazinger Z was lacking a lot of its special features at first and regularly had to be upgraded and re-outfitted with new equipment. At the same time, the manga introduced the Mazinger Army, a trio of weaker robots each designed to wield one of Mazinger's distinctive weapons. All three made minor appearances in the Mazinkaiser movie, and all three were destroyed, with only Million Alpha putting up any kind of a fight.
Averted in, of all things, Great Mazinger — the Mikene Empire get a hold of Great's plans and mass produce it perfectly (with the exception of its wings). They usually show up in any Super Robot Wars installment when the Great Mazinger storyline is used.
And it was also averted in Mazinkaiser: Shin Great Mazinger and Mazinkaiser are explicitly stated to be the finished models, their predecessors are the prototypes.
And averted in Shin Mazinger as Energer-Z was able to go toe to toe with Mazinger-Z.
Neon Genesis Evangelion does strange things with this trope. Units 00, 01, and 02 are referred to as the prototype unit, test unit, and production unit, respectively, but they're functionally identical in operation. End of Evangelion features "mass produced Evas" that are superior in basically every way, but aren't really a refinement of the original Evas so much as the same underlying technology taken in a different direction.
Sky Girls features this: The three original Sonic Divers are prototypes, and they do their job well. Subverted in the fact that the mass production model can do just as well, but the WORM attacks the production assembly plant, making the only one model that was completed a super prototype in its own way.
Also used straight when the Vic Vipers make their debut, it is marketed as cheap, much better and more heavily-armed alternative to the Sonic Divers that the titular characters use, and hence, is mass-produced. Not only it really is underperfoming in comparison, the best thing it can do is act as support rather than replacement. It actually even gets beaten by an old, conventional fighter piloted by the show's The Ace in the end, and it's a two-against-one battle.
Metal Armor Dragonar plays with this a bit. The beginning of the series shows the Dragonars as a set of stolen super prototype units, but their pilots are inexperienced, and the Ace Custom units trounce them frequently. After a while, the Dragonars are used as the template for a new Mass Production model that has specs stronger than any of the Dragonar units. However, after Professor Plato guides the heroes back to the military, the Dragonars are upgraded into Ace Custom Super Prototypes.
Pretty much the only mechs that accomplish anything important in Eureka Seven are super prototypes, with the two Nirvash (which are actually alive) units being the most prominent. There's also Holland's late-series mount, the TB-303 Devilfish, which is ridiculously powerful and has enough firepower to wipe out multiple capital ships, but requires the pilot to take life-threatening drugs to operate it... Aside from those, the rest of the powerful LFO's are all Ace Customs. Anything with "KLF" or "Mon-Soono" in its name is utter cannon fodder.
Sagara Sousuke of Full Metal Panic! handles the ARX-7 Arbalest◊, one of the first mecha to be fielded by MITHRIL to possess a Lambda Driver. Later in the series he goes up against many enemy mecha with Lamba Drivers of their own, but proves his to be the more powerful while defeating them in combat. It is suggested that this is because the Lambda Driver in Sousuke's mecha is a prototype model compared to the mass-produced variants fielded by the enemy, and is capable of increased output at the cost of stability. It does, indeed, fail to function properly on a number of occasions, leading Sousuke to become thoroughly frustrated with it. Said Lambda Driver is later put into the ARX-8 Laevatein which, despite the serial number, is actually an Ace Custom put together in a hurry. It can still kick the asses of everything mass-produced, though.
Partial subversion in Viper's Creed, in the last episode we see a prototype white mech with greater speed, armor and two additional arms; but its software is not optimized, so at critical moments it freezes from bugs.
Played straight in Outlaw Star. The XGP15A-II was purpose built using advanced military tech for the purpose of reaching the Galactic Leyline.
Clamp managed to do this in an episode of Angelic Layer to the titular toys when the design team unleashed against the tourney players a new prototype model with improved capabilities. Also, the original series can go to "Hypermode" which the later versions can't. Subverted by Shuko using a prototype that can barely move to beat the later version doll Wizard around like a, well, ragdoll even with vastly inferior tech and movements simply because she's that good.
Getter Robo Āḥ has mass-produced Getters who are nowhere near the godly power of Shin, who was too terrifyingly destructive to replicate. There's also the fact that limiting the amount of Getter Rays the machines can hold prevents them from turning sentient.
In Getter Robo Armageddon, Professor Saotome mass produces Getter Robo G in massive numbers with the sole purpose of forming them into Shin Dragon. Ryouma doesn't care and still beats the machines to a pulp.
The Hyper-Zoanoids in Guyver are, like ordinary Zoanoids, genetically-altered humans. The "hyper" designation is usually applied to prototype genetic templates, which are designed around an individual soldier's DNA; mass-production designs must be simplified to allow them to work on a wider range of humans, so the Hyper models tend to be considerably more powerful.
Genesic Gao Gaigar from GaoGaiGar FINAL — GaoGaiGar and GaoFightGar are both based on its blueprints, but are significantly weaker, partialy due to humans being unable to perfectly copy alien design, partialy on purpose, as some of original's weapons were modified to serve non-offensive purpose.
In Infinite Stratos, it turns out that Ichika's IS core is actually the very first one ever made. It's noted that the inventor "poured all [her] heart and soul into that core," since it was her first creation. Note that this is not the reason he can use the IS (he's the only male who can); rather, that is never revealed. Not even the original inventor understands why.
Houki's fourth-generation Aka Tsubaki might appear as an Ace Custom but one cannot forget that it was personally built by the inventor mentioned above and is thus guaranteed to be superior to future fourth-gen designs (for reference, various companies around the world have only begun prototyping and performance testing of third-gen IS units).
In Future GPX Cyber Formula, the Ogre AN-21 is the prototype to the Al-Zard NP-1. Ogre has the same bio-computer system as Al-Zard, but it also caused the deaths of 2 test drivers due to the fact the car was unable to satisfy the talent the bio-computer needed.
The Sizzlers of GunBuster are mass-produced versions of the Gunbuster itself, smaller and weaker (yet powerful enough to fight dozens of alien bugs easily!)
This happens when any villain tries to replicate a Super Serum. The first villain to try it is bigger, stronger, faster than the original, but the original never pushes it to the limits because of the idiocy-inducing effects of an overdose, or the subject becoming completely musclebound or even exploding. On the rare occasions that the villains continue to use the super serum on Mooks, they will have much smaller doses and usually be sent in groups.
Related to the above, Captain America is the super prototype for the Super Soldier program. Others are constantly trying to replicate his success with results ranging from mental retardation (Truth: Red, White and Black) to creating the Hulk (Ultimate Marvel) and the Weapon Plus program (Wolverine, aka Weapon X/Ten; Rogers is Weapon I).
Captain America's shield is a Super Prototype as well, being the precursor to adamantium. Adamantium is the attempt to recreate the material of his shield, but even primary adamantium is weaker than it.
The comic book version of Iron Man both subverts this trope and plays it straight. The subversion comes from Stark constantly producing improved models after the original prototype. The straight examples come from any even vaguely mass-produced derivatives, like the Guardsman armors, which are never on par with Iron Man's own gear. Of course, readers probably wouldn't want a bunch of glorified prison guards to be as powerful as the superhero.
And, in fact, it's explained that Iron Man himself doesn't want a bunch of glorified prison guards to be as powerful as he is. He deliberately withholds the best tech for himself and even goes so far as to build in exploitable weaknesses in case the armors are ever used against him. Considering the number of times Stark's technology has been stolen, duplicated or reverse-engineered, he's got a right to be paranoid and hold back technology. (Although, as seen in the Armor Wars story, sometimes he takes that right too far, beating up innocent people like Stingray and Captain America.)
In a way, the Hulk. While created by accident, Hulk was the first gamma mutant, and most following gamma beings (the Leader, the Abomination, Madman, Ravage, etc) were based off either recreating that accident or specifically copying his DNA. While some have had greater base-line strength than the Hulk, and most have retained their higher intelligence whereas the Hulk is most often shown to be a savage, Hulk's potential strength (increasing with anger) and his other abilities (Healing Factor, psychic resistance) have shown him to be the most powerful of the gamma beings.
Another factor in the Hulk's Super Prototype-ness is the fact that Bruce Banner psyche is so damaged because of abuse when he was a kid, it allows him to do whatever he wishes. Being a gamma beast meant unleashing a particular repressed trait. The reason the Hulk is stronger than the others? Because they're not as screwed up as Banner!
Super Dinosaur is superior to the successive Dino Men because of his armor which grants him unparalleled firepower.
In Sonic the Hedgehog, the Metal Sonic Troopers, Rotor and Uncle Chuck-designed and built Metal Sonics based off of the original Metal Sonic, are easily dispatched when they're turned against everyone, compared to the original Metal Sonic, who gave Sonic and co. a very hard time.
In Exoria, a modern-day ZeldaFan Fic, Epona is a prototype military motorcycle, codenamed MRX-402A (second prototype model of the fourth generation military reconnaissance X-series). Aside from being able to achieve speeds over three hundred kilometers per hour, it has onboard electronic systems that allow it to analyze the terrain ahead instantly and adjust the suspensions real-time. It also has an auto-drive function, and two .50 machine guns. Seatbelt not included.
In The Open Door, the Stiletto is the first craft built by newChaos as a test bed for the combination of the technologies available to them. Although officially rated as a frigate, it can punch far, far above its supposed weight. Eventually, with its long shakedown cruise over, its equipment receives rather drastic tonedown.
Subverted and defied in An Entry With A Bang!: The first GDI monitor is an unstable hodgepodge of Clancy-Earth and Battletech... uh, tech. The first prototype BearCat aerospace fighter is not mounting weapons. Both in-universe and at the writers' level, there has generally been agreement to take things slow and not do any funky stuff.
In Star Wars, Darth Vader's TIE fighter was a custom model with a distinct appearance. At least one Expanded Universe technical manual says it's one of a Low-Rate Initial Production batch of unsuccessful Super Prototypes; the design was rejected as too expensive and the TIE Interceptor was selected instead.
This was further explained in the Expanded Universe, specifically the TIE Fighter game. They had designed a model of Vader's TIE Advanced X1 that was intended for mass production, known as the TIE Avenger, but it and its successor, the TIE Defender, were shelved due to too many resources expended during internal civil war. Which was probably a good thing for the Rebels, seeing as how the Defender was widely considered to be the most advanced starfighter of its time.
The Trade Federation in The Phantom Menace uses two types of battle droids, that look the exact same. You have the OOM models, which possess advanced and independent programming, and the B1 models, which are dumb as a box of rocks. The kicker, the OOMs are the prototypes. You would think that with code being easily replicated, ALL battle droids would be OOMs, but instead the Trade Federation decided to shoot themselves in the foot.
Batman's costume in Batman Begins is a prototype armor suit that was rejected by the army because it was too expensive. The same with the batmobile, which was designed for jumping gaps to lay cables for bridges.
The RoboCop program arguably nailed the concept in ther first try, but failed to deliver a single functional/reliable cyborg after that. In RoboCop 2 a string of subsequent models fails in increasely gruesome ways - it turns out there are certain qualities the person must possess for the operation to work properly. Knowing this, the corporation resorted to a junkie drug lord with messiah complex as source material, reasoning that his addiction and vanity would help keep him in line (It Makes Sense in Context). The results were quite unsavory, to say the least.
Mythology and Religion
Apocryphally, Lilith. The first woman created by God, made of dust (like Adam) instead of being made from part of Adam. She wanted to be treated as Adam's equal but her strong will caused a bunch of relationship troubles, so they got divorced and God settled for a more passive production-model woman in Eve who would be more supportive (and/or more subservient) to Adam.
In Joel Shepherd's Cassandra Kresnov trilogy, the title character is a prototype of a new and improved version of the "GIs" used as soldiers in interstellar combat. The main improvement is in her intelligence rather than her physical capabilities. She is creative and capable of lateral thought, making her more flexible and independent than lower level GIs who mostly serve as grunts that follow orders.
In the Star Trek novel Final Frontier (no relation to the fifth movie), it was revealed that the Enterprise was the prototype for the Constitution class line. It was deliberately overbuilt, explaining how Kirk (and Scotty) could constantly push it past its design limits. Constitution ships-of-the-line were economized, resulting in them being more delicate ships.
The Long Shot in Larry Niven's Known Space 'verse is the only Quantum II hyperdrive ship ever built. Big motor in the biggest hull made left no room for profitable cargo.
In Daemon the first AutoM8 is an armoured, solid-tired Hummer that is Immune to Bullets. Later versions use normal cars as a base and are thus less survivable.
Mack Maloney's Wingman series makes liberal use of this trope, particularly in the case of Hawk Hunter, the titular Wingman. His main aircraft is arguably both a super prototype and an Ace Custom, as he usually flies an F-16XLnote only 2 were ever built which he has further modified with More Dakka and advanced avionics. When circumstances force the Wingman to use a different type of aircraft for more than a chapter, he will generally take the time to similarly customize his new plane, often even transplanting the avionics from his F-16 into the aircraft.
The Cool Starship equivalent is the USS Defiant in Star Trek: Deep Space Nine. In its debut, it took a dozen Jem'hadar attack ships (just three of which had shown themselves capable of easily destroying the previous most powerful ship in Starfleet) to disable the Defiant, and that was after it was heavily damaged in an ambush. Not to mention, they hadn't even worked all the bugs out of the design yet; in later appearances it was even more formidable. The specs indicated that it was about 1/10 the mass of the Enterprise-D yet carried armament equal to it. Starfleet eventually does make others which are apparently just as powerful (including a replacement for the original when the Dominion finally manages to destroy it), but it takes a while to get them into production.
Star Trek actually kept a pretty good eye on its tech level as various ships are introduced. The registry for the prototype ships usually have an NX prefix. The Excelsior was originally NX-2000 and was more of a testbed for the (ultimately failed) "Transwarp" engine more than anything else. Once the testing phase was over, she was given a proper NCC prefix. Otherwise, it didn't appear to completely outclass other starships like the Enterprise in terms of combat performance. In later series it seemed that the Excelsior design was actually one of the most versatile in terms of longevity, the design showed up as modern starships as late as Deep Space Nine's fourth season, more than 80 years after it was introduced.
The titular ship of Star Trek: Enterprise, the NX-01 Enterprise, also subverted the super prototype as her successor, the NX-02 Columbia, left drydock with capabilities that surpassed and were later retrofitted into Enterprise. Production designs for the uproduced fifth season of Enterprise and Word Of God statements from Doug Drexler recently revealed that the entire NX class was one big work-in-progress and that every ship was its own prototype, as evidenced by these sketches showing off the engineering hull that was to be added to the "NX-01.5".
Western subversion: Knight Rider: In "Trust Doesn't Rust", KARR takes KITT for an "inferior production-line model" and assumes himself to be a super prototype. He turns out not to have any apparent technological advantage over KITT (of course, KITT is hardly "production-line"), aside from a slightly improved speech module (In the next episode, KITT's is replaced by one similar to KARR's), though when KARR reappears in the third season, while still not more advanced than KITT, he does possess a number of features which KITT had only gained during the second season.
In the 2008 series, KARR is a Transforming Mecha, specifically designed for front-line combat. However, it was a failure, and a number of people died. KITT was designed as a car that could transform into other cars (e.g. a Mustang transforming into a pickup truck) and mainly designed for policing duties. However, the episode where KITT is shut down reveals that the military has always planned for KITT to be a temporary project. The goal was to have KITT develop as a fully-functional AI and then port that AI into KARR. The kicker? Both KARR and KITT have the same driver, the son of the original Michael Knight.
Power Rangers RPM has the Paleozords, abandoned mecha from the early days of Project Ranger. The reason they were abandoned is because the zord tech hinges on bio-energy fields of living beings, and the Paleozords (based on dinosaurs, as you might have guessed from the name) were trying to connect to creatures that no longer existed, which made them powerful but uncontrollable. By the time the Rangers rediscovered them, the technology had advanced enough to bring them under control.
In Power Rangers Time Force, the Quantum Ranger and his Quantasaurus Rex Zord were created during the early days of Time Force, and lost in an early time travel experiment until being rediscovered. However, they're quite stronger than the main five Rangers and any of their tech. However, there's a drawback: the main five have a DNA lock, so only you or your Identical Grandson can use it (hence Wes). The Quantum powers have a voice lock, making it easier for, say, the Monster of the Week to sic your Zord on the Rangers with just a voice imitation device.
In Denji Sentai Megaranger, the Megasilver suit is a lot stronger than the others... until we find out that its power only lasts two and a half minutes. (In Power Rangers in Space, the 2.5 minute problem existed for different reasons and the suit wasn't a prototype.)
Averted in Kamen Rider, but played straight in spin-off Kamen Rider Faiz, the Riot Troopers are nowhere as good as Faiz, though this may be due to Faiz being far more experienced and an extremely powerful Orphnoch to boot.
Also, the prototype Kamen Rider Birth suit in Kamen Rider OOO has fewer weapons than the main Birth suit.
Kamen Rider Wizard has Kamen Rider Beast, who uses an ancient belt while Wizard uses a modern one. Despite this, Beast's default form is as strong as Wizard's Mid-Season Upgrade form. However, he's also considerably less versatile, having far fewer magic rings than Wizard does (and it turns out Wizard can get far more use out of the rings he does have than Beast himself).
The Kamen Rider G3/G3-X armor from Kamen Rider Agito boils down to being this, especially after the introduction (and later mothballing) of the Kamen Rider G3 Mild armor.
The eponymous "super-sub" in Gerry Anderson's series Stingray (1964). All the other W.A.S.P. ships that we see are more-or-less conventional-looking (for the 1960s) submarines, and there is no indication that there is more than one of the class. Expanded Universe material in the TV Century 21 comic and official novels imply either that a second Stingray-class sub has been built (and enters service just in time to be stolen by the Mysterons) or that Stingray is an ungraded version of a standard W.A.S.P. patrol vessel with superior capabilities to its sister craft.
The Battlestar Galactica prequel Caprica features a super prototype, the first U87 Cylon equipped with a metacognitive processor displays the potential for near human autonomy. The problem with this is this level of intelligence is only achieved in a single prototype, if the MCP is placed in a different cylon it does not display sentience.
The Original Battlestar Galactica series had the C.O.R.A. Viper. Very fast, full A.I. computer piloting system, equipped for long range patrols, double the thrusting power of any other Viper — at the expense of the guns!
On Chuck, Chuck is the first successful Intersect and remains the only prototype due to repeated sabotage of the project. However, when they finally decide to create more Intersect agents, they turn out to be way too inflexible in their thinking and tend to overreact in combat situations.
A very odd version in Power Rangers RPM with the morphers. The morphers used by Gen and Genma are prototypes and thus do not carry the same energy limitations that the later versions used by the rest of the team.
The Brickspider Bot v1.0 of Dino Attack RPG is the original prototype of the Brickster-Bot Spiders that would later be mass-produced by OGEL Robotics, Inc. In comparison with the later models, the v1.0 is far more intelligent and cunning with its own distinct personality. This was deliberately toned down for the later models by its creators when they realized that something so intelligent would not want to act as a mere Mook.
Done in the BattleTech setting, which involves a lot of Lost Technology from the Star League era, technology which was only just catching up to where it had been around the time of the Clan invasion. Depending on the narrative era a Battletech game is set in, it is quite plausible to find older, more powerful versions of later knock-off technology.
Reversed with actual prototypes and test 'mech mounting new technology. These experimental 'mechs are typically more frail than a production model would be, as they were built for testing systems and not for fighting wars. So while digging up a 250 year old 'mech might get you a Super Prototype because you got a lost production model with better-than-modern-version lostech on it, building a new machine with experimental technology and putting it through the ringer will not get you similar results.
Oddly played straight by the first 'Mech in-universe. The MSK-5S "Mackie" is described as being less efficient that modern Humongus Mecha but published stats show it with weapons and engines identical to normal machines. Even weirder, it weighs in a 100 tons (the in-universe upper end of the weight scale) when many other 70 or 80 ton 'mechs have fluff that describe them as the biggest thing the technology of their era allowed anyone to build. So the first battlemech outweighed mecha that were built years later and had firepower and strength/weight engine power equal to everything that came after.
Since they're one of the only factions in Warhammer 40,000 whose technology is actually improving, the Tau exhibit this trope when it comes to their battlesuits. Ace battlesuit jockeys are given the chance to field-test advanced prototypes, and if a Tau commander does really well they may end up with their own Ace Custom suit. Unfortunately these shiny new features tend to come with a drawback or two, something notably absent in normal Tau technology.
This kinda applies to any sort of technology used by the Humans (of any faction). The most powerful weapons are inevitably some super-ancient prototype relic. Kind of hand-waved due to a.) the Adeptus Mechanicus's fear of inventing, b.) the relics themselves being of Alien origin and/or a sacred relic and c.) sometimes the owners flat out refuse to let anyone tinker around with their one-of-a-kind toy.
The Thunder Warriors are specifically stated to be cruder, more poorly armored versions of the process that creates modern Space Marines, but at the same time, a single Thunder Warrior is to a squad of marines what marines themselves are to a squad of regular guardsmen. Unfortunately they are nowhere near as stable, mentally or physically. The Emperor had them all (mostly) wiped out after conquering Earth in favor of the more reliable Space Marines.
Played straight with the Primarchs, who are superior to any other soldier the Imperium has and are the templates for almost all of the Space Marines in existence today. However, the process which created them were extremely intensive and the Emperor only managed to create 20 of them, which he later deemed to be used as the templates for the Space Marine Legions and commanders for said legions. They were, however, basically Designer Babies (from the Emperor's DNA himself) where Space Marines are people born normally with genetic engineering applied later.
Jovian Chronicles, Dream Pod 9's Gundam inspired setting, is naturally filled with them. A couple of the prototypes do get mass produced versions, but they pale in comparison to their predecessors.
This trope is prevalent in Magic on a more "meta" level: The designers are constantly trying to make more balanced versions of older, overpowered cards. Black Lotus, the original Moxen, and the original dual lands are among the game's many Super Prototypes.
Shadowrun introduced a trio of uber-powerful, almost godlike AIs. Once the Crash 2.0 hit and the three of them are (apparently) gone, AIs are now roughly as powerful as human hackers in the Matrix (to the point where they are options for player characters).
Appears in Heavy Gear, specifically as the background to the South's Gold Mamba design. The Gold Mamba was basically a prototype built at the same time as the common Black Mamba, but contrary to typical design theory (build something up until it works at the level you want), its designers approached it from the other side of the spectrum (put the most expensive equipment you can find on it and scale down until it doesn't work). This means that the Gold Mamba is an extremely powerful combat machine that is head and shoulders above the Black Mamba's performance, but ultimately it is extremely expensive and rare.
The proxies of Trinity were the first humans to become psions, and their psychic powers are noted to be significantly more powerful than later psions, as the process that created the proxies differed in important respects from the one used for other psions.
Proto Man of the Mega Man Classic series is usually depicted as being much more capable than the later model, Mega Man, and due to a bug in his design is the first robot in history to have full free will. On the flip-side, that same bug makes him far more vulnerable to damage and means his power reactor will catastrophically fail at some point (Implied to be quite soon in Megaman 10).
Mega Man X is himself a Super Prototype to all of the Reploids that were created afterwards. He was built with the ability to make his own decisions like Proto Man above, but was built with a "suffering circuit" that would allow him to weigh the consequences of his actions. This, plus over a century of self-checks made X a perfect machine. The Reploids that were built from his blueprints, however, lacked the same power of his suffering circuit and the checks, which caused them to become Mavericks/Irregulars.
Averted in Super Robot Wars 3. When you begin the game, the Getter Robo team is piloting the Proto-Getter Robo. instead of normal Getter Robo. When Proto-Getter attacks and doesn't kill an enemy, Ryouma gripes that the Proto-Getter is just weaker than the normal Getter and is actually happy when the original Getter is dropped in a few stages later.
In the Metal Gear series, the prototype Metal Gear RAY is of far superior quality to the mass-produced models later encountered by Raiden as a boss battle; then again, it may have been actually designed for its supposed purpose (to defeat REX derivatives) whereas the mass-produced versions were actually tactical defense units for Arsenal Gear.
In Metal Gear Rising: Revengeance Bladewolf, a prototype unmanned gear, is self-aware and pretty durable, while the mass-produced Fenrirs go down much faster and have less intelligence than a real dog.
The Delphinus from Skies of Arcadia is a possible example, but it's not entirely clear whether the weaker mass-produced equivalent (the Spectre-class battleships) are scaled-back mass production versions or the immediate predecessors of the Delphinus.
The Delphinus was a proof-of-concept model, but doesn't necessarily fit the trope, and THE Flagship for the entire Armada- it was overkill for the reason of it being an Ace Custom essentially.
The trope is directly subverted in the terms of the Moonstone Cannon. When you encounter the prototype, it's terrifyingly powerful. The Delphinus has the PRODUCTION Model of the weapon. It's easily several times as powerful as the "Test Cannon".
The real planes also have a bit of this. 5 in particular both subverts it (the F-15 S/MTD is better than the stock F-15 it was modified from) and plays it straight (the S-32 is better than the later Su-47)
Ace Combat X brought us the Fenrir. The original models had optical camoflage, ungodly maneuverability and a microwave weapon. the production models don't have any of that aside from the ungodly maneuverability at the cost of ammo. In the same vein, the Varcolac from Joint Assault is shown to have a rear mounted machine gun that shoots down any and all missiles that approach it. In game, it doesn't have that but it's still the best plane in the game if you give it the right mods.
The Smithy Gang in Super Mario RPG (Mack, Bowyer, Yaridovich and the Axem Rangers) are the super prototype models for their production lines. When you reach the last area, you discover that Smithy is creating an entire army of the bosses, though the Machine-Made versions are less powerful than the actual bosses.
The Edelweiss in Valkyria Chronicles, made by Isara's father for Welkin's father for the previous war. It was found to be an incredible tank, but it was too expensive for any kind of mass production.
Subject Delta BioShock 2 isn't just a Big Daddy — he's the first Big Daddy; unlike the production models, he's nimble and has plasmid powers. Yahtzee pokes fun at this trope in his review of the game. It's justified in-universe as his creators realized that Daddies like Delta are not only too costly to make but would potentially become too powerful to properly control. As such, the later ones were nerfed.
Vivi, like all Black Mages in Final Fantasy IX, is an animated doll. However, as the prototype model, his power is greater than that of his "brothers", and his lifespan is much longer, as well.
A Continuity Nod in Thunder Force series. The mass production model of Styx in III appear as NPC in IV; The Rynex in IV has its production model appear in VI and also serve as prototype of Gauntlet in V. It take Mid-Season Upgrade the Gauntlet into Ace Custom Vambrace and Mecha Expansion Pack Brigandine module that Earth's fighter can fight the Rynex. It's justified since Gauntlet is Earthling's replica, built with alien technology they aren't fully understand.
Final Fantasy VI's Kefka was the very first Magitek Knight (a normal human given magical powers by way of an infusion from an Esper). He consistently has much stronger magic then Celes, a later-generation Magitek Knight that joins your party.note The first time you fight him as a boss, he is Level 18, and has spells like Blizzara, Poison, Drain, and all three 1st level Fire, Ice, Lightning spells. Celes would only have Blizzard, Antidote, Imp, Cure, and Scan at that same level. Unfortunately, as a prototype, he was exposed to an imperfect version of the infusion process, which resulted in him going just a teensy bit insane.
In the Compilation of Final Fantasy VII, Sephiroth is a super prototype who is much stronger and more powerful than regular SOLDIERs and much more physically stable than the competing Project G prototypes Angeal and Genesis, who are subject to degradation. Unfortunately, Sephiroth could not be duplicated and he cannot replicate his genetic traits in monsters (like Angeal) or in humans (like Genesis).
An interesting version of this is in Fate/stay night. Gilgamesh has all the prototypes of every Servant's Noble Phantasm, and goes on to explain exactly why his prototypes are that much more powerful. However, this is subverted in Unlimited Blade Works when Shiro "traces" or copies all of Gilgamesh's super prototypes with his Reality Marble, essentially creating a water-downed mass production type version of each one; right after explaining although his versions are weaker imitations, there is no rule about the imitations losing to the originals, he states that he will prove his imitations are superior by destroying all of Gilgamesh's weapons and Gilgamesh himself. Cue Crowning Moment of Awesome.
Doubly Subverted, as every prototype of Gilgamesh's Gate of Babylon is in fact one rank higher than the actual Noble Phantasm (due to Nasuverse's Older Is Better rule), while the traced weapons are by default one rank lower, being copies. Shiro's advantage was in speed and quantity, not quality.
Triply subverted however, since Shiro/Archer could also overload their traced Noble Phantasms, making them Broken Phantasms, which would destroy them when they were used, but also raise them by a rank, effectively giving them the power of the original Noble Phantasm. Shiro's ability to use all of them as well as their original owners did, also gave him an advantage over Gilgamesh, who only knew how to use some, and just fired the rest as projectiles.
Front Mission 3 has a couple interesting examples. In the start of the game your character is a test pilot for Kirishima Heavy Industries and your first mission is actually a final test run of a new prototype Wanzer for the Japanese Military. The Shunyo Mk. 111 is far more powerful than the test Wanzers you fight against. The true Super Prototype of the game, though, is the Hoshun. This is a Wanzer that is somehow sent to you through the Internet and not only has more HP than any other pilotable Wanzer, but also has one of the only beam rifles in existence.
Interestingly, the starting wanzer Kazuki pilots, the Zenith RV (misromanized as Zenislev), is the super prototype of the next game, Front Mission 4, obtainable in Elsa's scenario. Since 4 canonically happens before 3, this indicates how much Wanzer development has progressed.
Prometheus, the last boss in Starsiege human campaign is the first Cybrid. For the Cybrid campaign, you become one once you reach the highest rank.
Phantasy Star Zero makes fun of this trope to a degree. Occasionally you will find messages with tips in them. A message talking about a particular robotic enemy in that area says, "Production model & Prototype. Do we need to spell out which one is more powerful?"
The backstory of Virtual-ON provides both aversions and straight examples. Some prototypes like Viper Alpha and Proto Temjin have inferior armaments to their production model. Original Fei Yen is much more powerful than the production model but is sentient and eventually runs away from lab.
Near the end of the first planet in Knights of the Old Republic, you get to win a swoop bike race on a bike modified with a prototype accelerator. The adversary tries to deny your prize on the grounds that it was an unfair advantage, but the prize, being a Jedi, takes matters into her own hands by breaking out and killing most of the bad guys.
However, this is justified in the background material: Factions entrust their newest tech to their most experienced and effective troops and crews; the actual equipment is not significantly different from that given to subsequent units. Furthermore, prototypes take longer to build (unless the base has a Skunkworks), indicating the extra resources needed to work out the kinks. The actual equipment is probably not a prototype at all, but first-generation production.
Fallout 3 has some really powerful prototype stuff. Example: MPLX Novasurge, a unique plasma pistol which greatly increases damage and the critical multiplier at the cost of doubled power usage and weight. It was developed by a "Section: A61" shortly before the Great War broke out. The prototype survived the war by being beamed aboard Mothership Zeta approx. 200 years before the Lone Wanderer found it in the ship's cargo hold.. Or the MP-47/A power armor prototype with a built-in medical dispenser and an onboard AI. And the Capital Wasteland's sole set of T-51b power armor(not counting the indestructible Winterized version from Operation: Anchorage). Finally, there's Liberty Prime, a Humongous Mecha built for the Anchorage Reclamation, but kept out of battle due to problems with its power supply.
Fallout: New Vegas shows that at least one prototype model of eyebots had a TV-screen, and not just a built-in radio. ED-E, however, is not quite this trope, despite being a prototype and much more powerful than its mass-produced cousins: it was the prototype to a series of combat-adapted eyebots that were scrapped in favor of Hellfire power armor, with the common eyebot being its predecessor rather than its successor.
There's also the Tesla-Beaton Prototype, a unique Tesla cannon, and the AER-14, a prototype Laser Rifle with a green laser. The Q-35 Matter Modulator is a Super Prototype and also has some backstory to Retcon why the FO 3 plasma rifle is so different from the original plasma rifle (dubbed the "Plasma Caster" in FNV): The plasma caster was too expensive, had an awkward form factor, and required too much training to be proficient in, so a military project was started to adapt it to a more familiar pistol-grip rifle form factor, and lower the cost.
Old World Blues has the Stealth Suit Mark II, which like the Medic Power Armor, has an onboard AI that automatically dispenses Med-X and Stimpaks.
A similar effect occurs with the Supreme Commander Experimental units. Any player will realize that these 'experiments' are always a great success, and utterly trounce dozens if not hundreds of the 'tested' units. And although you can build more than one of them, the too-expensive-justification is in full effect, as you need a very solid economy before you can start building one.
Happens in StarCraft II where a prototype superweapon called Odin is stolen from the Dominion. It doesn't just have more hit points than any other unit in the game and do more damage than anything short of hero units — it's also got several luxury amenities, including a restroom for the driver and an onboard nuke launcher. Rory Swann, the engineer of Hyperion, says it's too impractical to mass-produce, at least with the facilities available to Raynor's Raiders, so a scaled-down machine called a Thor is slated for mass production. (Oddly, the Dominion seems to have agreed with Swann, as the Odin is one of a kind and the Dominion only ever fields Thors aside from it.) There's also the Loki, a prototype for a new class of battleship, which boasts ridiculous firepower and toughness, completed at the same research station.
The Loki at least is destroyed, which may be why that never went anywhere.
In Command & Conquer: Red Alert 3, the KingOni is a hulking behemoth capable of bull-charging enemy tanks and shoot Eye Beams for the glory of the Empire of the Rising Sun. Apparently, the original King Oni is a super prototype, given to Emperor Yoshiro as a gift, which he uses when the enemy approaches his palace. It notably includes a set of Rocket Launchers for dealing with aerial threats, something the standard King Oni lacks. It's implied that this King Oni takes much more maintenance to take care of than the standard King Oni, but given that it's the emperor's personal machine, no expense was spared.
Played with by Prototype Jack in Tekken. While it's unknown what happened between him and Jack (both survived the original tournament), P. Jack was soundly scrapped by Jack-2 in Tekken 2. However, P. Jack's ability to fly was implemented in all subsequent playable Jack models.
In Vanquish, the ARS armor that Sam Gideon is wearing is a prototype of a new weapons system being developed by DARPA, and he is taking it along on the assault on Providence for two reasons: to test out its capabilities in live fire combat, and because the military is desperate for any weapon they can use to stop the colony's microwave array from being fired. In-game, it is indicated that the ARS has several limitations, primarily among them being that the suit will explode if it overheats too much.
The Excavated ATACs in Vanguard Bandits are super prototypes from which all basic ATACs were reverse-engineered.
Custom Robo is all about "ace customs" but your "super prototype" has a drawback for each advantage it has against mass produced robos of the same class.
The Unholy War has a regular unit called Razorfane, a robot that attacks with circular saw blades. One of the secret unlockable characters is called Betarazor, which is basically just an upgraded version of Razorfane, with more health and more powerfull attacks.
Invoked (but not in any meaningful manner) in Sonic Heroes. One of E-123 Omega's combo-score quips is "Worthless consumer models!"
Additionally, when he earns an E-Rank at the end of a stage, he laments that he "Couldn't even beat Gamma or Beta..."
Sonic Adventure 2 has the Biolizard, the prototype ultimate life form which was enormous compared to its successor Shadow the Hedgehog. It was locked in suspended animation by GUN until Dr. Eggman reactivated it in the process of inserting the Chaos Emeralds into the Eclipse Cannon and sent the ARK hurtling towards Earth, after which it was defeated by Shadow but recovered and merged with the Eclipse Cannon in order to ensure that the colony would fall, only to be defeated again by the combined efforts of Super Sonic and Super Shadow. It is subverted in that the Biolizard seems to suffer from severe asthma, and even with a huge life support system attached to it, it can't sustain combat for half a minute without getting tired.
Demonbane has this trope play on two examples. First is the Destroyer Robot, while the prototypes are still far inferior to Magitek-based Deus Machina, at least it can withstand some beating. The mass production model can be destroyed by Demonbane's head vulcan guns and one of them even got disabled by Winfield, who punched through its sensor camera, on foot. The second examples are various grimoire, their original appear as little girls with magic power, the copies are just books.
The eponymous armor from Vay has been copied and mass-produced by the Danek Empire to create their massive robotic army. However, once the five magic orbs are retrieved and the Vay Armor's power is fully realized, it can stand toe-to-toe with almost anything Danek can throw at it.
The Spartan-IIs of Halo serve as this to the Spartan-IIIs and IVs. The IIs tend to be larger, stronger, and just more naturally talented overall, due being subject to a much more stringent selection criteria than their successors. On top of all that, their MJOLNIR armor is far better than at least the III's SPI armor. On the other hand, the IIs were also much more costly to produce and equip, and the process of augmenting them had a much higher failure rate than with the IIIs and IVs, making them much fewer in numbers and much less expendable. Halo: Reach gives a good example of this trope, where Jorge, the Big Guy of Noble Team and its only Spartan-II, towers above his Spartan-III squadmates and effortlessly carries a giant machine gun that the others would be greatly slowed down by.
The IVs are superior in both equipment quality and numbers compared to the IIIs. However, while the former are highly-skilled volunteers drawn from the best veterans and recruits, the latter (and the IIs) were trained to be the perfect soldiers from childhood; this difference manifests itself most clearly in the somewhat unprofessional demeanor of some of the IVs.
Averted by the Spartan-I program, which did not have the success that the later programs did; if Sergeant Johnson is any indication, they're just slightly better than the best Badass Normals. In fact, the Spartan program as a whole had to be renamed from "Project Orion" in order to distance the S-IIs from their predecessors (who themselves were retroactively renamed "Spartan-Is" to acknowledge they did provide the necessary data for the success of the later programs).
Xenogears normally averts this trope, and hero Gears are usually either Ace Customs or relics of Lost Technology. The one major case of a prototype that's clearly superior to the followup model is Grahf's Alpha Weltall, which is built using 4000-year-old Lost Nanotechnology that can't be replicated in the modern world. Fei's Weltall is essentially a kitbashed knockoff designed by modern engineers, and is itself a Flawed Prototype; several of the compromises in the original design are patched out when Weltall is redesigned by Taura.
Shin Megami Tensei: Strange Journey has the insanely overpowered Lightning, which is in many ways a fully-retrofitted version of the game's standard dimensional-crossing warship. It's got even Reality Warper tech (too energy-consuming to move or deploy the plasma shield, but still...) even in-game, the difference between the Lightning and the other ships is is explicitly compared to a fully-tuned and upgraded car against one fresh from the dealership.
Zigzagged in the X series. Prototype vessels tend to fare differently than their production versions, some having quirks that make them better or worse (such as higher weapon energy recharge but lower rudder speed). That said, some ships designated as prototypes fit the trope: The Paranid Hyperion Vanguard is a limited prototype run of Corvettes that far eclipses all other corvette classes (Among its many advantages, its the only one that can carry fighters and is either the top or tied for top in terms of speed, durability, and offensive potential amongst M6 vessels). The Hyperion Vanguard never entered full production run however (Which is why they cannot be bought by the player - only acquired through boarding existing copies). And all prototype ships, once they're acquired, can be reverse-engineered and then produced in the Player Headquarters in practice like the factory-produced versions.
As one might expect from a Gundam game, Gihrens Greed has its share of Super Prototypes. However, it plays the "production cost" angle brutally straight; building an army of Gundams is prohibitively expensive, but a force of GMs will do the job at a fraction of the cost, so super mobile suits are best used as force multipliers in the hands of your aces.
This is actually mentioned with the Prototype Gundam Mk-II's backstory: the machine was stupidly powerful and was made with performance over cost in mind; thus, when it was done, it was a machine that couldn't be piloted unless you were extremely skilled (or a Newtype) and it cost as much as a fleet of Pegasus-class warshipsnote That's the same class as the White Base.
Wipeout2048 features unlockable prototypes which each has a huge drawback, but can be powerful compared to regular racers.
The first unlockable Prototype: The Feisar Prototype, can exceed massive speed but it only speeds up when hitting speed pads.
Second unlockable: The Auricom Prototype. It deals a decent amount of damage and doesn't get slowed down or wipes out when hit by a weapon. It can't pick up defensive weapons though and if you aren't carefull, you won't notice when your craft is on low energy.
Third unlockable: AG-Systems Prototype. Fast, ultra-agile and hard-hitting, but has the weakest shielding in the game.
Fourth unlockable: Qirex Prototype. Sacrifices normal weapons for a special cannon which is even more powerful than the Plasma Bolt itself.
Final unlockable: Pir-Hana Prototype. The fastest ship in the game hands down, but cannot steer without airbrakes.
Star Trek Online reveals that the prototype of the Advanced Escort ships, the U.S.S. Prometheus from Star Trek: Voyager was this, as the mass produced Advanced Escorts removed the the Multi-Vector Assault Mode (which allowed it to separate it into three parts) due to parts being easy to damage. Then, they put it back for the special variants.
For a fun thing, one of the purchasable add-ons is the NX prefix for all Federation ships. As it is cosmetic, there's nothing big about it beyond RP material, but with all the special high-ranking gear, you could pretty much say that you are flying a Super Prototype.
In The Adventures of Dr. McNinja, uberninja Mongo, the result of early ninja gene experimentation, wields chainsaw nunchucks and has "All the speed, agility, martial arts ability [of a ninja], combined with giant like strength and general insane awesomeness." The reason they didn't make more? It's too expensive. The "Inverse Ninja Law" is an actual in-universe force and the maker knows this, so that might also be a factor.
Gunnerkrigg Court has a room full of them. Most notably, the first robot of the Seraph series, S1, looks much better than the more recent ones. And it has actual hands, rather than the simple claws of the later S models. The explanation given is that, since the original designer died, no one (not even the prototypes themselves) understands the cutting-edge technology underpinning them (for example, these robots have no visible power source, or motor, or means of moving their limbs). The robots were forced to simplify their designs just for future robot generations to survive.
This trope is actually deconstructed in time. When one of the first generation robots is revived, he's impressed by the design of his descendants, because their simpler parts are more efficient and easier to repair.
From Girl Genius: The one or two Dingbots that Agatha has actually personally built, referred to as Dingbot Prime, are much better in every way than their successors. This is because most Dingbots are built by other Dingbots, and each generation is inferior to the previous one, leading inexorably to this trope.
There's twenty-six Ilivais prototypes that fit this to a T in Ilivais X (well, twenty-five, as A is anything but "super". They range from having slightly stronger weaponry to controlling six classical elements at once to being powered by a freaking Perpetual Motion Machine, but all of them are way more powerful than the MP units. The Aztecs hardly rely on them — their tactics are built specifically to best make use of a One-Man Army unit.
Starwalker: Starwalker was built to test a new drive system
Megas XLR is both a super prototype and an Ace Custom (so customized, in fact, that no one but Coop can pilot it, simply because he changed the controls that much). Megas was originally a Glorft design, stolen by Kiva.
The eponymous character in Generator Rex. Rex's nanites come from an earlier batch that had already received full programming and testing. The nanites that were spread all over the world in the Mass Empowering Event came from a later batch with incomplete programming.
Alpha, the Big Bad of the crossover with Ben 10, is a prototype model control nanite from when the creators were still working out a way to control the nanites. Alpha is so powerful he has the potential to destroy the world single-handedly!
The main character of My Life as a Teenage Robot is notably much smaller than the previous robot in the XJ line. She lampshades this in a late-series episode to which her creator explains that she had to cut down on her size to fit her personality in.
Roughnecks: Starship Troopers Chronicles has the Cybernetic Humanoid Assault System, or C.H.A.S; when introduced, it's a walking tank with heavy armour, enough strength to tear trooper bugs apart in hand-to-hand combat, a number of armaments, the sensors of a bomb-sniffing robot, and an "adaptive learning AI" — in essence, the ability to mentally grow and develop as a result of its experiences, something that leads it to performing a Heroic Sacrifice. Later versions, seen in a couple of episodes, are pretty much Mecha-Mooks and easily taken down by a single bug each. Justified when one remembers the end of the episode featuring the first C.H.A.S notes that the project was more or less scrapped because they were considered "less cost-effective" than human soldiers.
On expos showing new cars or military technology, the displayed products will almost always have superior stats or better looks than the finished versions. This however is because said prototypes, while more powerful, may have their stats so highpowered they become self-damaging from simply doing anything. Hence finished versions have to be toned down.
The world's first Nuclear Powered Aircraft Carrier, USS Enterprise (CVN-65) was a one of a kind super prototype of the later Nimitz Class carriers. Equipped with 8(!) nuclear reactors and advanced electronic systems on a unique square island structure the "Big E" was later surpassed in displacement by the Nimitz carriers, but remained the longest military vessel in the world until her retirement in 2013. The excessive cost of the Enterprise and its 8 reactor layout resulted in the Navy shelving the nuclear carrier concept with proposed sister ship USS America being re-ordered as a conventionally powered Kitty Hawk class carrier and the USS John F. Kennedy also being converted to conventional propulsion during construction. The US Navy would not commission another nuclear carrier until 13 years later in 1975.
Enterprise is the subject of a number of rumors about having an Up to Eleven top speed due to her large number of reactors with 50 knots the figure typically being cited. These are generally untrue with Enterprise achieving a 35 knot maximum speed like most other carriers, however the 8 reactor plant allows Enterprise to generate steam more quickly than her successors allowing for faster acceleration and less competition for steam between the catapults, electrical generators and engines.
The Pennsylvania Railroad was known to have built more than a few super prototype locomotives which were then never duplicated or scaled back for production. One of these was the class FF1 electric locomotive which was built in 1917 to test concepts related to electrifying steep mountain grades. Equipped with 4 1150hp synchronous AC motors the unit, nicknamed "Big Liz", developed a then astonishing 140,000 pounds of tractive effort. Unfortunately Big Liz turned out to be an example of Tim Taylor Technology. When pulling trains her power would pull out the couplers. When reassigned to pusher service Big Liz pushed with so much force that on one test train cars began to pop out of the middle. Big Liz was simply too much power in one locomotive for 1917 rolling stock.
In the UK, the Great Eastern Railway Class A55 Decapod: a steam locomotive built to match the acceleration of then-current electric trains. Built to prove a political point, the design never went into production.
Early models of a new-concept product such as a digital camera, being designed by-geeks-for-geeks, can sometimes have advanced features (foldout screens, own programming language) which get dropped in later models as the product goes mass-market. This can lead to howls of dismay from enthusiasts, who were expecting a new model to improve everything, only to find that a choice feature has been removed to save money or dumb-down the product for the average consumer.