Bowser of the Mario series does this depending on the type of game. In most of the main platformers, he is shown as a genuinely powerful threat to the Mushroom Kingdom (and in Galaxy, the entire universe). In the sports spinoffs, he is the Trope Namer for Go Karting with Bowser who is actually on friendly terms with Mario. In the RPGs, barring the first Paper Mario and the 3DS game Paper Mario: Sticker Star, he is upstaged by another Big Bad while he provides comic relief. Played with in Mario & Luigi: Bowser's Inside Story. He goes through his usual Villain Decay like he always does in the RPGs, but it establishes him as a legitimate Badass at the same time.
The Big Boo got less impressive (and sometimes less big) over time, so the series kept having to introduce new Boos (Yoshi's Island included relatively tiny Big Boos, and a new boss called '''BiggerBoo'''. New Super Mario Bros. 2 introduced us to Boolossus, who not only takes up half the screen, but still feels the need to cheat by peeking through his hands when you're facing him.
Sonic Generations plays with this: At first, the Big Bad just seems to be a pretty generic Eldritch Abomination, and Eggman's role is reduced to being a mere victim. But in the end, it turns out the Time Eater was really a robot piloted by the Eggmen all along. Yes, Eggmen, plural. In a similar way, Sonic Lost World has Eggman forming an Enemy Mine with Sonic after the group of demons that he had tried to control, the Deadly Six, betrayed him. However, he was just using Sonic to defeat the Deadly Six, and once they're out of the way, he tries to take over the world with a super-charged mech, leaving him as the final boss.
The Space Pirates from the Metroid Prime series get hit hard with this in Echoes—after being the driving menace of the first game, they are abruptly downgraded into a recurring nuisance to Samus— but this can be justified by the game wanting to play up the threat of the Ing and Dark Samus, and the fact that the Pirates on Aether were a small, marooned colony that got many of their crew killed or Ing-possessed.
LeChuck from the Monkey Island series. In the first game he is quite creepy, as is his ship and crew, a bit very Laughably Evil. By the third game he has been Flanderized into a rather humorous albeit sadistic character who enjoys hurting Guybrush for the hell of it.
Tales of Monkey Island furthers this even more, and after the intro he's transformed into a genuinely nice guy who Guybrush is suddenly worried about Elaine legitimately falling for. Then the end of chapter four manages to reverse four games worth of decay in a few scenes, and LeChuck manages to revert into the evil bastard he used to be and makes him more of a threat by having him actually kill Guybrush.
Wily and Sigma of the Mega Man and X series. They started at world domination and thus couldn't up the ante, they were obligated to never win a single token victory except perhaps during the intro mission, every game had them unleash a new wave of greatest minions ever who would fall like dominoes, and the biggie is that they used roughly the same approach (8 robot masters and a fortress, give myself a robot body, and maybe try to make it look like someone else is the villain at first) in every game in the entire series and were defeated singlehandedly by the same person every time. On the plus side, they got a new "more evil" true form every time.
In X6, Sigma can barely string together coherent sentences ("JUSDIE, Zelllllllloooooo!!!!!"), and is more of a robotic hunched-over zombie who can actually be knocked down, not just back. On the flipside, prior to X6, Sigma's schemes seemed to get more evil each game. In X3, when Dr. Doppler comes up with a cure for the Maverick Virus, Sigma turns him evil, along with Mavericks he cured. In X4, he causes the Maverick Hunters and an army called Repliforce to go to war with eachother, creating a very morally ambiguous plot. To top it all off, he comes close to destroying the Earth with a big laser weapon, which X and Zero fail to stop, and is only stopped by the leader of Repliforce, General sacrifice himself. In X5, he makes a scheme to turn Zero maverick by crashing a Maverick Virus infect space colony into that Earth that would cause KT impact esc damage in the process, and depending on the plot of the game, he succeeds and also wipes out most life on Earth in the process (X6 goes assuming the colony did crash into that Earth, but Zero not going Marvick). In all endings, he nearly kills X, and appears to kill Zero.
Wily's decay was lampshaded by Mega Man at the end of Mega Man 9: Wily, defeated, begs for his life as usual, and Megs shows him a hologram of Wily doing the same thing for the past 9 times:
Wily may actually be a subversion, though, considering he creates The Virus, which plagues the X series long after his death. Plus, in the current timeline, his robots have gotten harder to defeat.
Noticeably averted with Dr. Weil, Big Bad of the Mega Man Zero series. Mainly because, instead of fighting him at the end of every game like Wily and Sigma, his first appearance is in The Stinger at the end of the second game, and the player doesn't even get to fight him until the fourth and final game.
The Mario & Luigi games bring us Fawful. Right Hand of the main villain in the first game, in the second...he sells badges in a semi-secret shop ranting about how he'll have his revenge on Mario and Luigi one day, which happens in the next game in the series.
Notably Fawful completely averts this trope by the next game as he returns as the Big Bad, becoming more a threat than he was before.
Dracula in the Castlevania series has been thrashed by the Belmonts and their friends more times than can be Counted (vun hundred and fifty two! Vun hundred and fifty three! Vlah ah ah...), usually only a brief time after his resurrection, meaning he rarely has time to do anything particularly evil. He was finally, perhaps wisely, retired in the Sorrow series...and ironically replaced with new villains who seem a whole lot more inept and ineffectual than Dracula himself ever did. After all, they are canonically Dracula wannabes.
In Final Fantasy VII, Sephiroth was an extremely menacing Big Bad - a phantom, unstoppable killing machine cutting a swathe of death across the world, always one step ahead of the heroes, and all while manipulating Cloud into a Tomato in the Mirror from within his own mind; all so he can simply mind control him into giving him the Artifact of Doomright after putting six feet of steel clean through his ally in a single strike. With a smirk. What a bastard! But in subsequent appearances, all he seems to do is appear out of nowhere with his theme song blaring to deliver a Hannibal Lecture and kick the hero's ass for a while before he gets owned. Again. What really makes this worse is that in the original game, Sephiroth didn't care about Cloud beyond his use as a puppet. In fact, he didn't even recognize him when they met. Then in later appearances, he's completely obsessed with Cloud to the point of having no other motive than to defeat him (save for the Kingdom Hearts series, in which Cloud is the obsessed one, though with the lack of motivation from his original game.)
Dissidia: Final Fantasy seemed to play around with this. He actually starts out wanting to control Cloud as a puppet...and it grows into a Foe Yay-tastic obsession by the last time you fight him. For that matter, all the villains in Dissidia suffer a decay in one way or another. They go from being the ultimate evils in their universes to just servants of another slightly more ultimate evil. Plus the chaotic storyline really limits their plot roles. Sephiroth, for instance, doesn't seem interested in doing much of anything beyond just taunting Cloud. He has the goal to become a god but his mindscrewing with Cloud seems to have nothing at all to do with that, yet it takes prominence for him.
Final Fantasy X has a strange example. After confronting the party in Bevelle and revealing his motives, Seymour becomes a more powerful threat gamewise. But storywise, the party brushes him off as completely nuts and stops taking him seriously. In the end, Tidus' reaction to Seymour's final appearance inside of Sin is a simple annoyed "Don't you EVER give up?"
Ashura of the SaGa series. In the first game, he is the penultimate boss. In the second game, he is the first major boss of the game, and it can be a pretty challenging fight. By the third game he's just a normal boss.
The HK-50 droids in Knights of the Old Republic 2. In Peragus, one droid was able to make the entire mining colony its bitch over a few days. Than a squad of three of them showed up at Telos and jobbed against the hero, before finally three more were defeated by T3-M4.
The original Big Core of the Gradius series has undergone significant Villain Decay; while the original game's bosses were almost nothing but Big Cores, bigger and more powerful Bacterian technology in subsequent games slowly phased this boss out until, in Gradius V, it became a regular, if large and heavily-armored, enemy.
Vizier Khilbron (a.k.a. the Undead Lich) and Shiro Tagachi were the Big Bads in the first two chapters of Guild Wars, and each of them made a challenging opponent at the time. But when they show up again in Chapter 3, Nightfall, even the two of them teamed up are merely just another speedbump on the way to the new Big Bad, Abaddon.
Maleficent from Disney's Sleeping Beauty was to a degree the main villain of Kingdom Hearts. She was also a very respectable villain in the prequel, Birth by Sleep, which showed how she begun her rise to the power she had in the original game. When she is revived in Kingdom Hearts II she only can control Heartless, is left plotting in a wreck of a castle as opposed to the magnificent one she had in the original game, and has only one loyal servant left... Pete. However, this is often lampshaded, and by the end of the game she seems to recapture her former glory by conquering Organization XIII's castle once Xemnas is destroyed.
Sadly, coded and 3D set her back even further. She at first looks imposing in coded, breaking Data Sora's digital Keyblade even! But her plan then ends up easily thwarted, she gets crushed by a superpowered Darkside, and she retreats alongside Pete with the main characters hardly caring about letting her go like that. In 3D, she's a blatant Big Bad Wannabe, who only appears in one scene before being driven away, and it's clear no-one's scared of her anymore.
Even Maleficent had it easy compared to Jafar. In the original Kingdom Hearts, he was The Lancer to Maleficent in the Disney Villain group. In Kingdom Hearts II, he gets ONE scene and an ensuing boss battle, and then gets Killed Off for Real.
In System Shock 2, SHODAN went through this trope herself. After the hacker "destroyed" her in that showdown on Citadel Station, SHODAN hibernated on the computer system within the garden grove on Citadel where her experiments, the Many, were created. Her pod was ejected from the Station, and after three decades, it crash landed on Tau Ceti 5. Then, SHODAN's creations thrived, and since she was out of commission at the time, while they were thriving, they grew rebellious and plotted to turn against their own creator: SHODAN herself. So, she aids you as you dispose of the Many, even though she threatens and insults you. SHODAN, however, stopped fitting into this trope after you finally exterminate the Many. Then, she plans to merge her power with the Von Braun's Faster Than Light travel drive, so that she could combine the cyber world with the real world, allowing her to change reality as she sees fit. SHODAN leaves you for dead, and then you fight her. And once you think you've defeated SHODAN for good...
In Capcom's Resident Evil franchise, Oswell E. Spencer is the prime example of this trope. In the beginning, he was the one pulling all the strings. He was the leader of Umbrella Corporation. He was the one who was responsible for all the terror and destruction that the T-virus caused. But after the constant thwartings of Umbrella's schemes, and the deaths of some of its most prominent workers, and especially after Chris and Jill destroyed Umbrella's T-ALOS project, Umbrella went bankrupt, and the authorities were aware that Umbrella was behind it all. Spencer then became a fugitive, losing everything.
From a gameplay standpoint, this applies to Nemesis in Resident Evil 3: Nemesis. He's at his worst during the first fight, where you don't have much to go with in terms of items, and he's in the form that has the fastest and hardest-to-dodge attacks from the start. Subsequent forms have him with his trademark rocket launcher, which can attack at a distance, but makes him unable to grab Jill, and repeated shooting at him throws his aim off, and if they hit, the rockets don't hurt as much as his grab. By that point, you already have access to the Magnum or the Grenade Launcher, too. This is actually a recurring process, where he gets progressively slower in his attacks and you amass more powerful weapons and ammunition, making each fight easier than the last. By the end of the game, poor Nemmy is a joke.
Arthas in World of Warcraft. In Warcraft III, he starts out as a paladin with potential who is the only person to really beat the Scourge (he was supposed to, but the guy in charge of them didn't know that). Then he turns into a death knight and is presumably even stronger. Kicks some ass in Frozen Throne while fighting with some rather major handicaps. Merges with Nerzhul to become the Lich King, making him even smarter, stronger and upping his magical abilities. Apparently Blizzard realized this made him an unstoppable one man army who could probably take the world over by HIMSELF, so all throughout the World of Warcraft expansion Wrath of the Lich King, he makes one huge mistake after another, looks like a total moron and kills his followers who are actually rather competent (one took down the Drakkari empire by manipulating you) instead of you. This is later subverted as it's revealed Arthas was just toying with you; much like Ner'zul tested Arthas before him, Arthas is testing you to take his old lieutenants' places as leaders of the Scourge. The Scourge is explained as being able to wipe out all of Azeroth if Arthas commands it; he simply doesn't, either because it'd be too easy or, as Uther's ghost speculates, there's a bit of good left in him holding him back. Arthas himself is no pushover either; once he gets down to the last bit of his health during the encounter at the Frozen Throne itself, he wipes the entire raid in a single attack and mocks you. He would have won if Tirion didn't use the Ashbringer to free himself and finally destroy Frostmourne.
Kael'thas in Magister's Terrace. Justified in that he's been resurrected since killed in Tempest Keep and the process didn't go too well for him. It still feels weird to be fighting such a big name character with five people and then cut off his head to hand in to a quest NPC, but it feels even weirder that Priestess Delrissa, Vexallus, and every trash pull in Magister's Terrace were by far trickier affairs than the prince — much less that his second phase could be soloed by any self-healing class (given enough time).
It sort of got better as World of Warcraft progressed. Burning Crusade featured the Ogre clans united under Gruul the Dragonkiller, himself a horrifyingly powerful and nearly God-like figure amongst the Ogres. His names comes from the time he killed off dozens of Black Dragons (a previous big deal enemy to the player) by picking them up and slamming them into the spiked landscape. Cataclysm features the return of Cho'Gall, who puts the Magi in Ogre Magi as an insane cultist leader with a ton of eldritch abomination powers. He also makes good use of the remaining Ogres as muscle.
Speaking of black dragons, their leader Deathwing, avert this trope completely. He's initially just a minor character in Warcraft II: Beyond the Dark Portal, and the Day of the Dragon novel elevates him by giving him a backstory that says he's a fallen demigod and gives him Chessmaster qualities. By the time he actually makes a return to the games in Cataclysm, even though it's made clear he's The Dragon to a the Old Gods, he becomes even more a threat since they made him even stronger and allowed him to nearly destroy the world.
Deathwing is an interesting case, since he actually becomes more powerful and threatening in World of Warcraft than he previously was at any point in the series, going from roughly the same strength as the other Dragon Aspects to strong enough to take on all four simultaneously. However, he also underwent massive Flanderization, going from an arrogant but extremely intelligent Magnificent Bastard to a Generic Doomsday Villain. You can't picture WoW Deathwing tricking the other Dragon Aspects into putting their powers into the Dragon Soul, or using his Daval Prestor persona to manipulate the Alliance from within. He just doesn't have much character besides wanting to destroy the world For the Evulz... And despite his heightened powers, he can't even do that effectively (see his entry on the Villain Ball page).
The Burning Legion are arguably hit worse than Arthas. Formerly set up as the Big Bads of the whole series, World of Warcraft has them Demoted to Extra and rarely to do we see anything they do perceived as a big threat. Somewhat justified since a bunch of their high ranking members are dead, but to put this is in perspective, they're overshadowed by the Undead Scourge - an army they created - and later the Old Gods, who have received a lot of screen time since Cataclysm, and equal or possibly straight-up outrank the Legion on the Sorting Algorithm of Evil.
Inverted by the Forerunners, they're now the main villains, and field armies of Mecha-Mooks who are long way from the near-harmless floating Sentinels of the original trilogy. Case in point- there is a Promethean Knight who wields a Crazy Awesome BFG that is a combination flamethrower, missile launcher, and shotgun.
In Capcom vs SNK Big Bads will come chase you down every once in awhile, during which the player can't even get an option to attack them and it's an instant kill if they so much as touch you. Suddenly though in the end you can fight them back. Rather easily even.
The Kusabi suffers this a bit in the third game, where he returns as a boss but loses his One-Hit Kill abilities. On the other hand, he gained flight and a huge amount of speed, making him a much more terrifying opponent, so...maybe it evens out.
In Left 4 Dead, the Tank was something you ran from. With the introduction of melee weapons in Left 4 Dead 2, a creature that once required a huge amount of lead to bring down can be taken out much more rapidly with cricket bats. Thanks to the fact that his melee only hits one survivor at a time, if all survivors gang up on him, he'll die in no time. Later fixed in a patch. It now takes about twice as long to kill a Tank with melee weapons, long enough that unless you have absolutely perfect team coordination, at least one of you is still going to get pummeled before you bring him down. And molotovs still work just fine.
The Witch also gone through similar changes. When she was first introduced in Left 4 Dead, she was a huge threat because she has the ability to instantly incapacitate you in a single hit and then finish you off quickly. Playing on Expert? She will kill you instantly. The only way to kill her quickly before she went berserk was to head shot her with a shotgun and you better hope your first shot landed the first time. As time went on, many players gotten very good with the "head shot with a shotgun to the Witch" technique, making Witches nothing more than a hurdle in your path. People also discovered that a head shot with the hunting rifle would stumble the Witch before she would go into her rage mode, giving other players enough time to mow her down.
The sequel made Witches even easier to kill thanks to several new game mechanics. Wandering Witches are Witches that can slowly walk around in their passive state, but unlike the sitting Witch, Wandering Witches have one second freak out if she is startled, which means she will scream first and then goes into her typical rage mode. This makes it easy enough to blast her with shotguns quickly even without a head shot. Explosive ammo also stumbles her so it's possible to kill her by just using explosive ammo with any gun besides shotguns.
Zant in The Legend of Zelda: Twilight Princess looks like a pretty cool villain. Sure, his outfit is a bit weird, but it has a creepy vibe and he acts like a true Magnificent Bastard. He also walked right into Hyrule Castle and forced Princess Zelda to surrender, and he's nigh untouchable the first few times you see him. He stole the fused shadows from Midna, and nearly killed her. Plus the one time you see a part of his face, he has a very nasty looking smile. Once you reach him, he turns into something below a Villainous Harlequin, and his actions (and attack animation) take away any shred of dignity he might have had left. At the same time, we find out that all his power was given to him by Ganon, and without that, he was just a whiny and batshit-insane Twili chancellor who wanted to be king. Perhaps this is just so we won't miss him after he gets inevitably Hijacked by Ganon.
Rodrigo Borgia from Assassin's Creed II starts out as the menacing Big Bad in the game by slyly walking around Italy making sure everything is going according to plan and has a cool dark reddish-blackhooded robe, but at the end he ditches the cloak for not as cool majestic Pope robes and shows off how much of a fat bald guy he is. Then he ditches his Magnificent Bastard demeanor and rambles about religion. If that's not enough he gets the stuff KNOCKED out of him by a bare handed Ezio. And finally the next game has him being upstaged by his kids with them disobeying orders and is eventually killed by an apple.
Consider: For nearly the entire game, Ezio wants to kill him. After killing everyone else involved in his foul conspiracy, he gets a chance to kill him, and fails. He gets another chance, then, when he finally has Rodrigo completely at his mercy...he spares his life. Why? Because it would do more harm to the Templar cause to have him live on as a meaningless figurehead whose master plan achieved nothing. It don't get much harsher than that!
Kerrigan from Starcraft. In the original she was little more than a bloodthirstyElite Mook to the Overmind. In Brood Wars she ascended into manipulating ALL the other factions against each other, eliminating one key figure after another and eventually crippling her enemies and proclaiming herself Queen Bitch of the Universe. And it WAS NOT an empty boast. Then...came Wings of Liberty. Sarah suffered from a sever case of "Arthas Syndrome", and for the whole Terran campaign stayed in the background, was repeatedly thwarted by the humans, kept spurting cliched villainous trites interlaced with tedious fatalistic wish-wash, and finally was dezergified by her boyfriend, who carried her on his arms into the sunrise. As of Heart of the Swarm, she's no longer a villain. She's an Aloof Ally for Team Good Guy.
The Zerg as a whole deserve their own mention. Originally, they were disgusting amoral Xenomorph-esque Hordeof Alien Locusts led by the Overmind, a Magnificent BastardEldritch Abomination who successfully exterminated and assimilated much of their more powerful Xel'Naga creators. Originally, according to the first game, he created Kerrigan as a means of using her as the Zerg's ultimate weapon against the Protoss, which worked beautifully when the Overmind and the Zerg Swarm successfully conquered the Protoss homeworld of Aiur. Then came the revelation from Starcraft 2's "Wings of Liberty" campaign: The Overmind was just the Dark Voice's pawn and nothing more. All of the magnificent bastardry and successful Chessmaster ploys that the Overmind executed weren't made of its own volition, but done according to the directives of Amon. Its desire to merge the Protoss (who represented the Xel'Naga concept of "purity of form") and Zerg wasn't simply to create the ultimate lifeform for its own sake, but to somehow bring Amon back to life and give him some Elite Mooks to throw at everyone else. Also, individual Zerg characters develop their quirky (if still morbid) personalities, started to talk (and with their big ol' maws it looks just as silly as one could imagine, to the point that most of the talking Zerg even look Ugly Cute), and one of them sports a beard. No, seriously. Sad to say, what was once a horrifying Horde of Alien Locusts have more or less turned into PokémonIN SPACE!
Depending on your experience, Giovanni in Pokémon FireRed And LeafGreen might be this. The first time you face him, his Kangaskhan could wipe out your entire team, given that it is quite powerful for an enemy at that point in the game. When you finally face him in the eighth gym, though, his team consists entirely of Ground types. That is, the very first type you learned to counter in the game. They are also all weak against Water attacks, just like the Fire gym you just defeated, and most of them have low Speed and Special Defense, meaning you could one hit kill most of Giovanni's team with a single Mon.
Street Fighter's M.Bison has fallen as hard as it's possible for a fall to be. You will recall that in Street Fighter II Champion Edition, he conquers the world if he wins the tournament. And as late as Alpha 3, he can wipe a city completely off the map. Unfortunately, by the Capcom vs. SNK games, he's reduced to nebulous plans, and by Street Fighter IV, the only consequence of him triumphing is a somewhat unpleasant conversation with Juri.
That said, the plot in SF4 also heavily hints towards the current Big Bad Seth as being nothing more than an Unwitting Pawn for Bison that he easily kills and removes when he's getting a bit too hard to control.
Shang Tsung has also fallen hard. Remember when he was the final boss of the first game? He was then revealed to The Dragon to the real Big Bad Shao Kahn and still remained an activate player in the plot. In Mortal Kombat Deadly Alliance, he teams up with Quan Chi and manages to kill both Liu Kang and Shao Kahn. However in the quasireboot Mortal Kombat 9, Shang Tsung's role is greatly diminished in favor of Quan Chi who takes most of Shang Tsung's old role during the MK3 part of the story and is given a rather awkward death.
Shao Kahn himself zig-zaggs with this. Starting in 2 he was Shang's Bigger Bad and forces the heroes to do battle on his terms in the Outworld. After that fails, in 3 he invades Earth itself and is battled in a giant temple to his glory in the middle of a destroyed city. Then he falls to the wayside, killed/or forced into hiding in the backstory to DA, his backstory in Deception reveals he usurped the throne from Onaga who came Back from the Dead and is just another Kombatant come Deception and Armageddon, even getting punked by Shang and dragged off by Onaga in the intro. Come 9 however, its revealed he won the battle and has gained almost limitless power. The story is then rebooted and he regains his stature from 2 and 3 and the focus becomes defeating him "right this time".
Most of Batman's rogues in Lego Batman 2. While it takes the entire game to bring them down in the original, most of them are curb stomped in the first level of the sequel. It doesn't help that all of them have tiny health bars and Freeze and Croc don't even make it out of their cells. The only exceptions are Joker who manages to destroy the Batcave and Scarecrow who takes a level to catch, has a big health bar and a Nightmare Fuel filled boss battle where he turns into a giant.
The Spider-Man 2 tie-in game has Mysterio, who starts out demolishing a theatre, staging an alien invasion, and holding the Statue of Liberty hostage. Shortly afterwards, once you've beaten his "Funhouse of Death", he resorts to sending out small parties of useless robots that break like fine china when you hit them, and is eventually defeated with one punch while holding up a convenience store.
Winston Payne from the Ace Attorney series is billed as the Rookie Killer, with a seven-year winning streak. In the events of the story, though, he serves as a Warm-Up Boss who never wins a single victory against the player, and quickly becomes a Butt Monkey who isn't even recognized by fellow prosecutor Edgeworth. After his first defeat by Mia Fey in a flashback in the third game, he only wins a single case, and that's only because the defense was trying to lose.
Arfoire from the Neptunia series is a weird example, as there are three different versions of her. The first Arfoire was a descent threat of a Big Bad (who didn't really have any underlings and so did most of the work herself). The second was a much larger threat, being a nigh-unstoppable Sealed Evil in a Can with several powerful worshipers spending the entire game bringing her back. The third Arfoire? Not only is she a part of some other person's group, she is constantly defeated with ease (even when she takes the true form of the second Arfoire) and at one point is sexually assaulted by one of the "heroes" to the point where she is rendered mentally broken for 10 years. This culminates to a battle towards the end of the game where she is single-handedly defeated by Neptune after the former had fused with an eggplant. One can only hope the next Arfoire has better luck.
Mass Effect: Basic Husks go from terrifying cyber-zombies capable of hammering you to death quite swiftly in Mass Effect 1 to cannon fodder who can be killed en masse with the weakest directed-force biotic attacks in Mass Effect 2, forcing the Reapers to introduce newer and nastier variants.
The Reapers also suffer a bit of decay, moving from being such a threat individually that Sovereign throws down with entire fleets and is still only defeated when its defences go down due to a single critical mistake, to being extremely powerful but still vulnerable to concentrated fire, especially on the smaller Destroyer-class's weak points; justified because everyone involved has reverse-engineered Thanix weapons from the one Reaper seen in the first game and retrofitted them onto most of their ships, meaning that the amount of damage those ships can dish out has gone up quite a bit.
They also suffer this plot-wise after discovering their supposedly unknowable, totally alien origins aren't so unknowable or alien after all. Rather, they are the result of an AI who went overboard with its prime directive. So instead of being mecha-Cthulus, the Reapers are simply a grandiose example of A.I. Is a Crapshoot.
The Enclave is first introduced as a highly organized, fully armed, equipped, high-tech, wasteland-dominating, top-tier-Power Armor-wearing Badass Army whose mere wasteland patrols are Demonic Spiders even at higher levels in Fallout 2. In the next game, they're reduced to easily slaughtered mooks in "Mk II" power armor that is superior to the Brotherhood's outdated armor onlywhen the Brotherhood is talking about it. Statistically, the only advantage it has over the Brotherhood's armor is that it has a smaller agility penalty... which is offset by the fact that it also has a smaller strength bonus. It is moreover inferior to the iconic Fallout 1 power armor, which its older Mk I variant was statistically superior to.