Multiple instances show up in the various Star Trek series:
The Borg are probably the most infamous example, gradually going from a once-a-season menace to a routine annoyance. In their original appearance in the Star Trek: The Next Generation episode "Q Who?", they were a faceless, inscrutable Hive Mind who could never be truly defeated because they always acted in perfect synchronicity, and could never be reasoned or bargained with. This gradually changed with "I, Borg" and Star Trek: First Contact, which presented the idea that the Borg could be taught to act as individuals, and introduced the Borg Queen as a physical leader figure whose defeat could provide an easy way to resolve plots. Then came Star Trek: Voyager, which took place entirely in the Delta Quadrant (the site of the Borg's home territory), thus making the Borg regular antagonists for the first time in the franchise's history. Since tangles with the Borg suddenly became frequent occurrences, the writers of Voyager had to regularly depict them being defeated by the crew of the titular lone starship (in contrast to appearances in previous shows, where the Borg mopped the floor with entire fleets) in order to keep the story moving, thus robbing them of a good deal of their original scare value.
Species 8472 were Scary Dogmatic Aliens until "In the Flesh". They were introduced as a terrifying telepathic species of aliens from a place called "fluidic space", a race so xenophobic that they tried to exterminate all other life because they considered it impure. They traveled in bio-organic ships that could destroy Borg cubes like a photon torpedo could destroy a Ford Pinto and these ships could combine energy weapons to blow up a Borg planet. Except not, because they're retconned to be a peaceloving people beneath the surface, and were only fighting the Borg in self-defense.
The Ferengi were downgraded from serious threats to comic-relief pests after only two appearances. The Ferengi were intended to be major recurring villains, but over the course of several makeup revisions, the Ferengi went from impressive to goofy-looking. This probably has as much to do with the fact that when the Ferengi were introduced early on in Next Generation, Gene Roddenberry was still involved with the production, and was trying as hard as possible to recreate the old series. However, characters that would have worked as villains in the much cheesier era of the original series just inspired laughter in modern audiences. Also, all else being equal it's easier to make tall guys look threatening than short guys. Roddenberry really wanted to have villains who are small in stature yet still dangerous, but it just didn't work out. Not that their status as Strawman Capitalists helped much either.
Q turned from a frivolous yet dangerous omniscient being who nevertheless delivered some important Aesops to Captain Picard, to a lovesick puppy who goes to Captain Janeway for advice on parental relationships and conflict resolution in the Q Continuum. Q really was one of those characters who were a case of Depending on the Writer, especially in TNG. He's creepy and borderline sadistic in "Encounter at Farpoint", then campy and unwittingly annoying in "QPid", then he's back to being sinister in "True Q". It's debatable whether or not he was even actually a villain, considering how many times he (sometimes indirectly) helped Picard and the crew.
The Dominion in Deep Space Nine suffer heavily from this trope as well. In Starfleet's first military encounter with them, three of the weakest Dominion fighters destroy the Galaxy-class USS Odyssey, ostensibly one of Starfleet's most powerful ships, with relative ease. By the end of the show we can see Galaxy-class starships destroy the Dominion fighters in one shot. note That said Deep Space Nine relied unapologetically on Conservation of Ninjutsu and Rule of Drama for all fights, often having wildly inconsistent or improbable results compared to the rest of the franchise and its own series. There is an in-story justification in "The Ship", though: a particular Vorta by the name of Kilana allowed the Federation to get its hands on a more-or-less intact Jem'Hadar fighter. The Starfleet Corps of Engineers did the rest and at the two powers' very next combat encounter, most of their old tricks, e.g. shield-piercing weapons, suddenly don't work.
The Dominion got a bump in threat after the Breen joined and brought in a weapon thatvdrained all the enrgy in a ship and rendered them helpless. Then it dropped again, with another in-story justification as the Klingons accudentally stumbled onto a countermeasure that the Federation and Romulans were able to duplicate after a few months.
After seeing how much respect the Borg lost during his writing stint on Voyager, Ronald D. Moore rather neatly avoided the trope in his remake of Battlestar Galactica. The villainous Cylons are only sparingly used as a direct threat to the heroes, and typically when the heroes do beat them there's some kind of price. However, one particular Cylon, Caprica-Six has decayed rather badly. Given she was only in one episode (the miniseries), where she performed one mercy killing and lectured Baltar and that was it, and then wasn't seen again until the late second season where she followed through on being sad at taking a baby's life by regretting the holocaust in its entirety and missed a man she from the beginning cared about, or why else bother to save him, she didn't have much badass to decay anyway.
Almost every season of Power Rangers begins with the villain being replaced by a new one — because after 40 episodes of losing, the old villain doesn't seem as cool.
Serpentera goes from destroying a planet, to being ineffective because the bad guys don't know how to keep it powered, to destroyed by a motorcycle (albeit a motorcycle from god).
Goldar (who might be considered The Dragon to both Rita and Zedd) was an excellent case. In early episodes, he was a nighmarish opponent, more than a match for all five Rangers at once. But once he lost the element of surprise and they got accustomed to him, he slowly lost his edge. Jason handed him his first true defeat, and then Tommy handed him another. Around the time of Rita and Zedd's wedding, he had become little more of a joke and a parody of himself.
Rito Revolto was an extreme example. In his first battle with the Rangers, he handed them a sound defeat, destroying both the Thunder Megazord and the Tigerzord. Unfortunately for him, he got his clock cleaned by them in their second battle (once they replaced the destroyed Zords with the Ninjazords) and after that, he wasn't able to do anything right.
Happened often in MMPR seasons two and three given how often they reused the monster suits; a monster who nearly killed the Rangers in its original appearance would often return to be defeated with a single blow or be incapacitated with slapstick.
Pretty much inevitable for any of the recurring villains on Doctor Who.
This was the fate that befell the Doctor's greatest enemies the Daleks after 16 television stories, four cameos and countless appearances in other adaptations, especially when their creator, Davros, began to dominate the stories. They were later made more menacing again; in 1988 they were given the ability to fly, and for their 2005 return in "Dalek", they were given new abilities, such as a force field and the ability to crush a man's head using the plunger arm. However, they may be falling back into this, going in their more recent appearances from one being defeated by its own self-loathing, to a fleet being defeated by a Deus ex Machina, to millions being defeated by reversing the polarity. On the other hand four Daleks, later three Daleks and a Dalek-Human hybrid take two episodes to destroy. Because of this, it seems the Daleks suffer from some variation of the Inverse Ninja Law. The more there are, the easier they are to defeat.
Another weird example of limp Daleks is "The Chase" - while what they are doing on paper is very threatening (they have mastered time travel and are out for Revenge!), due to the story being an especially silly comedy Out-of-Genre Experience they come across as relatively harmless. They fall off things, one stammers "Um, er, er," when questioned by its Drill Sergeant Nasty superior, and they get defeated by amusement park animatronics before being mowed down by the Mechanoids. This was possibly given some Foreshadowing in the preceding story, "The Space Museum", in which the Doctor's companion Vicki confesses she finds Daleks to be quite cute. Fortunately, the Daleks go back to an improved version of their original, menacing characterisation in the next Dalek storyline, "The Daleks' Master Plan".
This was even lampshaded by Steven Moffatt, who commented that they had lost to the Doctor "400 times" This was probably exaggeration, but he does have a point as the Daleks have only won ONCE over the past few years - and even then, the only thing they "won" was the chance to run away rather than inflict any serious damage. For this reason he is temporarily retiring the Daleks, probably for a good couple of seasons. Considering that they have appeared ten times since the show's revival, it's certainly fair enough. And in the first episode under him the Daleks actually win by tricking the Doctor into enabling their race to be restored.
The Master particularly suffered from this, with many writers simply using him as a convenient bad guy with little motivation beyond being "eeeevil". The trend arguably started from his very first appearances, since he appeared as the Big Bad in every episode of Season Eight of the classic series, which arguably diluted his effectiveness right from the off. He always allied with another evil power, which then betrayed him, forcing him to work with the Doctor. Over his many appearances in both classic and new series, writers have tried most of the tricks above to avert Villain Decay, including threat escalation, frequent Enemy Mine plots, Alternate Universe victories, and having him murder the family members of series regulars. Probably for the same reasons that the series itself has been so long-lived, despite succumbing to Villain Decay several times over, the character somehow keeps bouncing back as a Magnificent Bastard. The new series attempted to correct this both by giving him a plausible motivation - complete insanity - and by showing how badass he could be; not least by stranding the Doctor at the end of time itself, becoming Prime Minister of Great Britain, massacring a tenth of the population of Earth and all in all being a rather Magnificent Bastard before the Doctor managed to undo everything.
This trope was partially justified for the Master after the Third Doctor's era. He has reached the end of his regenerative cycle and is stuck in a decaying body, so spends his next two appearances, during the 4th Doctor's era, trying to get a new body. After getting one, in the next story he (accidentally) destroys a quarter of the Universe after (deliberately) going on a killing spree in Logopolis. And he brings about the 4th Doctor's death.
In his next appearance in "The End of Time", due to a botched resurrection he becomes more crazy and is left more concerned with eating to keep his body stable. He succeeds in turning most of humanity into copies of himself, however he is revealed to have been manipulated by Rassilon, who easily turns everybody back. The Master then saves the Doctor.
The Master's worst period for this covered his two appearances in the Sixth Doctor's era, "The Mark of the Rani" and "The Ultimate Foe" (in which he is not the title character), in both of which he achieves very little and is used as comic relief for the Doctor's confrontations with entirely new Time Lord villains. This was recovered to a degree in his final old-school appearance, "Survival", in which his tendency to kill people for lulz was played up and taken extremely seriously as repugnant villainy instead of comedy.
In a possible way to avert this trope, Steven Moffat says that when the Master reappeared in Series 8 she needed to kill someone to show how dangerous she was. Sure enough Missy disintegratesAudience SurrogateFangirl Osgood, while taunting her about it. Then crushes Osgood's glasses beneath her heel. However sadly at the end of the episode The Master hands the Doctor his victory which for some fans undermined her menace once again
The Cybermen were Doctor Who's most egregious victim of this trope. In Second Doctor Cybermen stories, they were powerful, some might say too powerful. That may be a good reason they weren't used for the entire Third Doctor run. When they were brought back at the beginning of the Fourth Doctor era, they were given a weakness: gold dust would clog their chest units and suffocate them. All well and good, until someone misinterpreted that to mean that gold itself was their weakness. In Earthshock it wasn't so bad, as only one was killed, and that weapon (Adric's badge) broke and was unusable. Despite their gold weakness not coming up in The Five Doctors and Attack of the Cybermen, they were still killed in heavy droves by Rassilon's tower's defenses, the Raston Warrior Robot, and even human weapons. The weakness returned with a vengeance in Silver Nemesis, however, treating us to the wonderful sight of Ace killing Cybermen with gold coins fired from a slingshot. The Cybermen seen that come from a parallel Earth do not have this weakness, and the ones from this universe that returned in the new series were no longer defeated that way (although one flagship was entirely destroyed by the Doctor as part of The Teaser of "A Good Man Goes to War").
Don't think the new series doesn't get in on the action. In their first appearance, they're a great menace and put the parallel Earth in a constant state of Robot War reminiscent of post-Judgment Day scenes in the Terminator franchise. Their second has them effortlessly brushed out of main villain role by the Daleks - quite a sucker punch to fans who expected an Ultimate Showdown of Ultimate Destiny if the Dalek and Cybermen ever met (really. Some people had been waiting for it since before the show was in color. Finally we get it and it turns out Cybermen have no better luck with the Daleks than the Redshirt Army and their Five Rounds Rapid.) Every appearance since has had that "getting emotions back is bad" thing mean "turn off the central gadget that suppresses emotions or give any partially-assimilated person a pep talk and all Cybermen drop dead." By this point, fans of the Cybermen will long for the days when you had to run out of gold coins to slingshot at them at some point.
In "Dark Water/Death in Heaven" the Cybermen are reduced to just Mooks for the Master.
The only time the Cybermen get to be properly badass after their reintroduction is "Nightmare in Silver," where none of their weaknesses can be brought to bear in a way that lets you kill 'em all at once, and they're faster. All the doctor can do is play for time. In the end, the king of the planet evacuates it, destroys it, and everyone runs away. Dayum.)
This trope was one of the reasons why the Mandragora were not used in a story in The Sarah Jane Adventures as it was felt they would be defeated "too easily" (and so were replaced with the Ancient Lights).
Justified with the Macra. When they first appeared in "The Macra Terror" in 1966 they were a cunning enemy that were controlling a human colony without the humans realising. When they appeared in "Gridlock" in 2007 they were much larger, but now savage beasts that lived at the bottom of a Motorway, snatching vehicles that came too close. However Gridlock is set billions of years later when they have devolved into savage beasts.
A very weird mixture of this trope played straight and this trope inversed occurs with the Weeping Angels. As the show has gone on, they've gotten more powerful and dangerous, while at the same time, the audience has found them less and less scary: 1. In "Blink" they had an extremely disturbing appearance and behavior that caused them to be deemed the most terrifying Who villain of all time, but all they did was send people back in time a few decades and they had a weakness that they couldn't move while being looked at (and therefore if two or more caught sight of one another at the same time, they'd be frozen like that forever). 2. In "The Time of Angels"/"Flesh and Stone", they appear to have lost the weakness for each other's sight (although they still freeze when a person looks at them), they kill prolifically in the dark, any image of them becomes an angel itself, and if stared at too long, they infect the person looking at them and turn them into an Angel. However, the overwhelming response to this episode was that they were far less scary than in "Blink", partly due to Conservation of Ninjutsu, and partly due to stylistic/directorial issues that stripped some of their mystery (such as acquiring the ability to communicate and moving onscreen, thereby breaking the conceit that the viewers gaze functioned like a character's gaze). This is granted very debatable within the fanbase (as with many things), but the point still stands. 3. In "The Angels Take Manhattan", they became an even crueler villain, sending people back in time when they entered a room, trapping them in a room for the rest of that person's life, and luring the past version of the person into the room just when their future self was on the brink of death, in a temporal loop that they fed off of. Yet once more, fan reaction deemed that they had lost all scariness and mystery, due to the same reasons as the previous episode and due to massive plot holes that made them seem ridiculous (such as the Statue of Liberty being an Angel). 4. In "The Time of the Doctor" they are reduced to merely a cameo. When one touches Clara she isn't even sent back in time, and the Doctor and Clara first escape by summoning the TARDIS round them, then the Doctor stops one with a mirror.
This seems to have happened to the Silents. Their plans extended to before they first appeared, with them blowing up the TARDIS and nearly causing the Universe to be erased from existence, which was the Story Arc through Series 5. When they appeared in the two part opening to Series 6 they quickly became one of the most popular villains, having invaded Earth and been manipulating humanity for thousands of years. However their rather confusing and convoluted plan made them seem less of a threat later in the series. Finally in "The Time of the Doctor" though the Silence appear it is claimed the Silents from before were a renegade faction and the main Silents eventually work with the Doctor.
Rassilon is on the receiving end of this hard in Hell Bent. In previous stories, Rassilon was one of the Big Bads of the Doctor Who Universe, a rarely-seen but immensely powerful and influential villain, the corrupt co-founder of Time Lord society, a Mad Scientist of such staggering genius that he made his fellow Time Lords seem dimwitted by comparison, and obsessed with immortality. Come the Series 9 finale, however, and this once impressive villain has regenerated from Timothy Dalton into Donald Sumpter, with the new interpretation coming off as an ineffectual, whiny, ranting old man who can do little more than ramble about his supposed invincibility, threaten (but not actually kill) people with his gauntlet, and froth with rage about the Doctor doing Doctor-y stuff. He gets defeated in about fifteen minutes via the Doctor simply staring him down, convincing all of his minions to abandon him, and booting him off of Gallifrey.
In Buffy the Vampire Slayer, the Turok-Han (ancient ugly vampires) of Season 7. The first one that shows up beats Buffy all by itself, but by the end of the season everyone is hacking them down left and right.
Plus the Vampires themselves, who constitute a major threat in the first season, becoming progressively weaker until finally they're just a bunch of wussy mooks that even Xander has roughly even odds of killing in a fair fight. This was briefly Zig Zagged in later seasons where Riley had to become a Super Soldier just to keep up, but overall in both Buffy and the spinoff, Angel, Vampires went from "Major threat that requires an incredibly superhuman girl to be born every generation just to deal with them" to "A random passerby can take one out with a pencil". They're still treated by the characters like they're a major threat, but the actual quality of the threat tends to be far inferior to how much they act like it's a threat, as exemplified by their strength being wildly inconsistent; sometimes being portrayed as being far above any normal human's and at other times they can be easily overpowered and restrained by a young (non-Slayer) woman who can't weigh more than 120 pounds.
Inverted in Angel. Wolfram & Hart, the Big Bad for the first two seasons, starts out as an evil organization for the underdog protagonist to rise up against, but are in actuality an Invincible Villain, as Holland Manners states that their goal is not to win, but to endure and be fueled and preserved by the evil that lies in all of humanity. As long as humanity exists, good can never win, and Wolfram & Hart will have nigh ultimate power.
That being said, in Season 3 they become secondary antagonists to Holtz and Sahjhan, and are portrayed as generally craven and incompetent. It gets even worse in Season 4, where their LA offices are destroyed and the staff killed by the Beast. And then backtracked when they let the team run the rebuilt LA branch in season 5 just to keep them busy; nothing in that theater of operations ultimately affected them at all.
Nicole Wallace of Law & Order: Criminal Intent started off as Moriarty to Bobby Goren's Sherlock Holmes, which made her getting nailed in her return appearance so satisfying. Then she was brought back in increasingly ridiculous ways, to the point where she was closer to a supervillain than her original anti-Goren persona. The Villain Decay reaches its nadir in her final appearance, in which she's just a Red Herring for the real villain, who kills her offscreen.
The Source of All Evil in Charmed undergoes sudden and severe decay between seasons 3 and 4. After a well executed gambit at the end of season 3 that leaves two Charmed Ones dying and one trapped in the underworld, everything falls apart. He does manage to kill Prue, but only because her actress was leaving the show. Then he's revealed to be comically reliant on a Seer ally to the degree that without her telling him what's going to happen, he can't even predict that Leo, whose entire purpose in life is to protect the Charmed Ones, might try to rescue the one he has trapped, which he does offscreen. After that he screws up his attempt to turn Paige evil by being incredibly obvious, gets severely wounded by one renegade demon throwing fireballs at him, and eventually loses not just his wings but the menacing hood as well and reveals a goofy face before dying. Three not mutually exclusive explanations for this are: they wrote the season 3 finale without knowing how they were going to resolve it; the loss of a main actress forced them to do a hasty rewrite and devote a lot of the screentime that would have been devoted to a satisfying followup to introducing a new character; and while it was fine for the Source to be competent and powerful as a background Bigger Bad, if he was going to bring the fight to the Charmed Ones then one party needed to have a major competence shift, and it's easier to write down than up.
Any and all demonic threats in general suffered from villain decay; early demons, albeit being a Monster of the Week in most cases, were a threat to the sisters individually; later on, when all-purpose vanquishing potions were produced by the gallon, they were mere nuisances most of the time. Perhaps this is why villains in later seasons consisted of one of the Elders who supposedly oversaw all "good magic," beings capable of removing people from reality at their whim, and finally, other witches.
Scorpius in Farscape managed to remain a Magnificent Bastard throughout the second and third seasons, thanks in large part to the writers letting him achieve total victory in the second season finale. The third season thus became about the heroes trying to reverse their earlier loss. However, by the end of the third season the show introduced a new villain who served as Scorpius' superior, and the first few episodes of the fourth season saw him apparently lose all his fearsomeness, with Grayza and Braca dragging him around on a leash like a dog, occasionally forcing him to lick Grayza's boot! For a time, he even looked as though he was becoming one of the heroes, with the only concession towards his original magnificence being somehow able to get himself (begrudgingly) accepted as a part of the hero's crew even though he freely admits that his goals and motivations haven't changed a jot since when he last tried to kill everyone. And then the whole descent into mediocrity turns out be a subversion: not only does he backstab Crichton so masterfully that it takes him two episodes to figure out what happened, but he manages to neatly counter Crichton's attempt to backstab him back. He's even pretending to be a double-agent for the Scarrans, fooling the Emperor himself into believing that Scorpius had been employed by him for years. For good measure, it turns out that Braca was on his side after all, and the "dragged around on a leash" thing was just another part of Scorpy's masterplan.
In the first season, the early-on Big Bad was Bialar Crais, the senior local Peacekeeper who was chasing them because he blamed Crichton for his brother's demise. He is usurped (and ruined, professionally) by Scorpius at the end of Season 1 but reappears later and becomes (uncomfortably for all) a semi-crew member due to his symbiotic relationship with Moya's child.
Harvey (the neural clone of Scorpius inside Crichton's head) was specifically introduced to avoid this trope. This way Scorpius could appear as a constant threat without downgrading this menace by having Crichton escape at the end of the episode.
The clone itself was subjected to extreme villain decay when the chip that generated it was removed from Crichton's head. While it did survive this, it lost all ability to control Crichton, and its personality degenerated from an exact clone of Scorpius to something that bore at least as much resemblance to Crichton.
Grayza began to suffer decay as the Scarrans became the main villains of season four- and ended up kidnapped by them due to her own gullibility. Particularly blatant was the revelation that Captain Braca- who she'd supposedly enslaved with her infallible pheromone glands — was actually still working for Scorpius; he went on to personally remove her from command to prove it. And just to rub it in, her command carrier was retaken by Scorpius, who'd recovered from his bout of villain decay.
Shows up quite a bit in the Stargate-verse. In the interest of fairness, it does have to be granted that there's a justification for aliens suffering some decay, in that part of the SG teams' missions is to promote Villain Decay; that is, a large part of the purpose of the Stargate program is to go forth and find out what's out there, and ways to defend Earth from those threats. If they were at all successful, Villain Decay was simply the logical extension of their success.
Stargate SG-1 fits this trope like a Goa'uld hand device. The Goa'uld were introduced as merciless, brutal and could effortlessly obliterate Earth as well as having a firm grip on much of the galaxy, held back only by in-fighting caused by their lust for power. When our heroes encounter just a small group of Jaffa, they manage to escape in one piece if lucky. But as the series progressed they became a bunch of arrogant, scheming, childish fools with a Napoleon complex and their mighty Jaffa armies become P90 fodder. Their flanged voices sounded cool and creepy when spoken slowly and calmly, but sounded ridiculous when they put any real emotion into it. By the end of the series, a Goa'uld encounter is just an inconvenience as our heroes have bigger fish to fry.
The TV movie Stargate Continuum attempted to reset the Goa'uld villain status by having Ba'al go back in time and prevent the creation of the Stargate program and using his knowledge of the future to unify the Goa'uld under his rule (he also casually executes Apophis, the first true major villain in the series, while Apophis's brother Ra, supposedly the ultimate System Lord, is just one of his lackeys). It seems to work, as there is absolutely nothing Earth (without alien tech) can do against a fleet of Goa'uld ships in orbit. Indeed, the only solution is to go back in time and prevent Ba'al's change.
In the original Stargate movie, the heroes only fought one Jaffa one-on-one (well, two or three on one, really) and then only really survived because Daniel ringed down in the exact right place at the exact right time. Since that's not exactly a viable tactic for an ongoing series, the Jaffa get progressively wimpier as the show goes on. Free Jaffa, however, seem much more badass than their enslaved counterparts, partially because there are fewer of them, and therefore the writers don't have to worry about tipping the scales too much. The Jaffa's increasing status as mooks was later lampshaded, with Jack pointing out that Jaffa weapons and tactics are meant to terrorise populations into obedience, whereas P-90s are weapons made to kill.
The Replicators, on the other hand, largely avert this trope, as each time the heroes meet a bunch of those things, it has required an even more insane plan than the last one to merely stall them. Trapping them in a time-stop bubble (they escape), sending then into a black hole (escape too), finding a ancient-made BFG specially designed to destroy them (become immune) and friggin' finally, using a weapon that can fry the entire Milky Way to destroy them all at the same time once and for all. Their Asuran brethren in Atlantis required a similarly insane plan to put them down once and for all.
The Wraith in Stargate Atlantis also went the way of the Goa'uld, as first the Atlantis Expedition develop a retrovirus to turn Wraith into humans, but then get reduced to in-fighting amongst themselves over dwindling food (read: human) resources. The Wraith lost their powers to cause hallucinations after their first appearance. Even though they can regenerate from wounds quickly, their scab-masked grunts quickly become just so much cannon fodder. Back around "The Lost Boys" (season 2), it was a difficult prospect for a small team to infiltrate a Wraith hive; by the later seasons ("The Queen" or "The Shrine"), the good guys are almost nonchalant about walking into Wraith territory. This wasn't helped by the introduction of the new Big Bads on the block, the Asurans (who were really just the Replicators, but less threatening). Part of the reason for the Wraith's decay was that they had to be weak and fragmented enough to not be able to simply curb-stomp the isolated Atlantis expedition. However when Atlantis regained contact with Earth, the Wraith threat became increasingly ridiculous, especially the idea that they were any sort of threat to the milky way considering the large amount of factions present there that could easily wipe the floor with them.
The Grand Finale shows that the Wraith are one ZPM away from becoming a nigh-unstoppable threat. The Super-Hive they create with just one of those oversized batteries can mop the floor with any ships and can take a hit from a weapon capable of One-Hit Kill Ori motherships with minimal damage (that the organic armor heals quickly). Even Atlantis itself barely manages to stall the Super-Hive for a few minutes and nearly crashes as a result.
As shown in Stargate Universe, the Lucian Alliance is doing the opposite, rising from a fairly weak cartel to a major opponent to Earth, starting a Space Cold War at which they're very successful. They even manage to upgrade their previously-weak Ha'taks to be able to match Earth's Asgard-improved ships. It turns out Earth humans aren't the only ones who can be smart. (The writers even addressed this: when asked about how the original-film-era pyramid ships that became So Last Seasonmany seasons ago can match the Asgard-improved ships, the answer was simply that the whole universe hadn't stood still while Earth made improvements.)
Adam Monroe, formerly Big Bad of season 2. When he returned in Season 3, he was downgraded from a Magnificent Bastard to comic relief. Then he was killed off by the new villain, Mr. Petrelli, in an Eviler Than Thou moment. Oh, and all this took less than two episodes, possibly setting a new record for 'fastest villain decay ever'.
Mr. Sweeny on Ned's Declassified School Survival Guide, to the point where he doesn't rat Ned out in the finale for sneaking along on the field trip. He leaves him stuck in that tree... "but do tell me how your day turns out."
Dr. Smith on Lost in Space may be one of the most iconic examples of this trope. He was originally a dangerously intelligent saboteur attempting to kill the Robinsons, but by a few episodes in he had deteriorated to complete pest/buffoon status. Early attempts at character development soon puttered out, and he became simply annoying comic relief. This was a rare case of intentional villain decay. Jonathan Harris, and the show's writers, realized very quickly that the Robinsons would never have tolerated the much darker Smith from the pilot staying around. In comparison, he's a much more series threat in the film, especially once he turns into a Half-Human Hybrid.
Wizards of Waverly Place: The mummy wasn't nearly as badass in "Wizards vs. Werewolves" as he was in the "Chronicles of Moises" arc, and his defeat was ridiculously easy.
Ben Linus from Lost, through a mix of Sorting Algorithm of Evil and Character Development. In seasons 2 and 3, he comes across as the ultimate in Magnificent Bastardry (and he's still got most of those skills), but season 4 saw the introduction of his arch-nemesis, Charles Widmore, and the conclusion of season 5 reveals that Ben has been the Man in Black's unwitting pawn all along. Adding to that, circumstances saw Ben becoming the Losties' Token Evil Teammate from season 4 onwards. But in this case, Villain Decay doesn't preclude being awesome, thanks to Ben's always-entertaining approach to solving problems and Michael Emerson's award-winning performance, and despite working with the Losties for three seasons he doesn't actually make a Heel–Face Turn until season 6's "Dr. Linus".
Brad Bellick of Prison Break. Corrupt Cop and Smug Snake in season 1, he serves as the main antagonist there and was quite cunning. He becomes much less of a threat in season 2. When season 3 sets in, he's completely pathetic, being the lowest of the low in Sona prison and being treated like shit by everyone. In season 4, he joins the protagonists and pulls a Heroic Sacrifice. Everyone mourns for him, apparently having completely forgotten what an utter bastard he was in the first season.
Partly due to Seinfeld Is Unfunny, Jerri Manthey. She was seen as the original survivor villain mostly because she was the first to be called that. (Richard Hatch is probably more of the "original" survivor villain) She was actually booed off the stage in All Stars, yet years later after the likes of Boston Rob controlling the game, Russell Hantz sociopathically pushing his way to the finals and admittedly griefing his fellow players, Jonny Fairplay lying to get a sympathetic advantage, Ami Cusack, and players like Naonka, Corrine, and Randy just being a Jerk Ass...When Jerri showed up on stage in Heroes vs. Villains and wasn't like any of those, people actually applauded for her.
Jonny Fairplay went from the notorious liar of Pearl Islands to first voted out in Micronesia because he wanted to be with his wife and daughter. (He wasn't lying!)
Omen on Dark Oracle. In Season 1 he managed to be the Big Bad, even with his powers sealed. In Season 2 he returns with his powers unlocked...and is demoted to being a flunky of Blaze and Violet. He's still dangerous, but Lance and Cally have bigger fish to fry, and simply aren't scared of him anymore. In the end, he's reduced to a rather pitiful figure who pulls a Heel–Face Turn to help Cally and then dies.
A brilliant example of Tropes Are Not Bad from The Wire. In the first season the Barksdale crew ruled the West Side of Baltimore. By the third season, they were in a tit-for-tat and being matched by independent drug lord who had no backing and was young and inexperienced. Marlo's ruthlessness surprised even Avon but it went beyond that, particularly with the collapse of Avon and Stringer's friendship where the cracks could be seen as early as the beginning of the second season.
It was also thoroughly justified since most of Barksdale's muscle and key lieutenants were put in jail at the end of season 1. Without them, Barksdale has to try to run a criminal empire only using guys that were lucky enough to avoid the mass arrests, too unimportant for the police to bother with, or inexperienced newcomers replacing the old guys.
Crowley's character arc has taken a few weird turns over the seasons to the point where he zigzaggs the trope. He was genuinely threatening in season 5-7 and a rare demon who avoids the Villain Ball, but not above entering an Enemy Mine with the Winchesters solely for his own benefit. In season 8 he became more evil than ever, capping it off with trying to kill everyone the Winchesters have ever saved. Due to a partial demon cure trial, he becomes a lot more emotional in season 9, and spends most of his time chained up in a cellar. His position is all but usurped by Abaddon, and the Winchesters openly express their disgust at how inconsequential the supposed King of Hell has become. Then a gambit of Crowley's played out at season's end - Dean is now a Demon, and in Crowley's claws. This is eventually lampshaded when his mother rants that he's not the king of hell but the Winchesters' bitch.
The Leviathans. When Castiel was their host, Leviathans were Ax-Crazy, frightening, mysterious Eldritch Abominations dripping black ooze who Death liked, probably because they were implied to be the things that inspired H.P. Lovecraft's stories. Although the writers tried to keep them menacing throughout the season, they misused them constantly, and their leader became fodder for constant dick jokes. That's quite a fall from their not-too-far-off early days. The Decay was reversed in the Season 8 Purgatory flashbacks where the Leviathans could make genuinely intimidating antagonists again, but Jeremy Carver (the season's show runner) opted to not use them outside of said flashbacks.
The Demons as a whole. In an early episode, the brother have trouble to stop a single one from crashing planes but in later seasons more powerful variants are introduced which leaves the lesser one as random mooks the brothers or their allies easily capture offscreen to interrogate them.
The angel Metatron expels the angels at the end of season 8, is the Big Bad of season 9 where he manipulates the angels into killing each others and temporally kills Dean in the finale. However in season 10, despite his successful escape from Heaven's jail, he becomes a minor nuisance and tries to hid himself. In season 11, Cas even has pity of Metatron and spares him when he has the opportunity to kill him.
This happens to many reappearing villains in crossover and anniversary events of long-running tokusatsu like Super Sentai and Kamen Rider. While the general rule of thumb is that resurrected villains are always weaker than they were originally, it is still quite jarring to see top-tier bad guys like Shadow Moon and Apollo Geist getting defeated in less than a minute.
It goes both ways, though: While they're defeated much more quickly, the crossovers became such Massively Multiplayer Crossover affairs that the number of heroes they face make them seem a lot stronger, as well. Each of these villains were long-running foes of one hero, eventually defeated in one-on-one combat. Now you've got these same guys effortlessly handling multiple Riders or Sentai teams or multiple Riders and multiple Sentai teams at once until they manage to defeat them using powers they didn't have in the original series. Doras from Kamen Rider ZO is the best example: the fight against him in the Kamen Rider Decade finale movie doesn't last two full minutes, but it consists of him handing thirteen Riders a Curb-Stomp Battle. To beat him they all (well, the ten who had them) had to use their Super Mode, two using their super-er modes that they didn't get until Decade. This makes Doras the single most powerful enemy in Kamen Rider history, something no one Rider could have ever taken even (in the case of Kuuga) using powers that could supposedly destroy a whole planet.
Captain Hook in Once Upon a Time. In season two he was a ruthless man obsessed with vengeance that even manages to pull a Batman Gambit over on Rumplestiltskin himself. However, come season three, he was reduced to little more than a lovesick puppy following Emma around without any of his former edge. He later recovers villain cred after Emma makes him the Dark One without his consent. He then becomes the Big Bad and proves extremely dangerous and clever but only for two episodes, whereafter he is promptly killed by Emma.
Most antagonists in Scrubs do this, since we learn more about them. Dr. Kelso, for example, starts out as a harsh jerk, who loves making people feel small, especially Ted, but after he retires, he mellows out considerably, to the point that he and Dr. Cox, who had argued with him all the time, became best friends.