The first Teenage Mutant Ninja Turtles animated series used heavy Lampshade Hanging ("at last, Shredder, you've done something right!") to underscore how completely the Shredder had become a joke villain. While he was mildly threatening in the first season (although to what extent this is the case is cause for debate), villain decay set in very quickly after that, as it did with most of the series' villains.
The Shredder of the secondTeenage Mutant Ninja Turtles cartoon series, on the other hand, managed to emerge after seven seasons mostly unscathed by villain decay, growing more powerful to the point where the turtles stopped being able to defeat him with martial arts alone, and always portrayed as both scarily competent and pure evil. However, not all the series villains are so lucky—the Shredder's dragon, Hun, in particular, went from "tough" to "joke" in the space of one season, before regaining some measure of respectability during the last third of the show's second season, which he retains—mostly by not featuring him in any extended battles with the turtles—until the end of the show... and gains a considerable power upgrade upon becoming an Empowered Badass Normal in Turtles Forever. Karai went from beating all four turtles and Casey Jones (easily) in her first appearance to Leo and Mike making a complete mockery of her in her own base when all they were there to do was steal an Ancient Artifact.
Sideshow Bob didn't suffer from this until many seasons into the show. His subsequent appearances always outdid the last and became a lot more violent and heinous, but he still never won. Around his fifth or sixth appearance he lost it though.
Even worse, Mr. Burns used to be a greedy, heartless, megalomaniac Corrupt Corporate Executive, the villain of many episodes. He was regularly depicted as decrepit and with the mindset of a more reactionary era, but that didn't stop him from being entertainingly pure evil. Come Season 10 and beyond, he was inexplicably transformed into an inoffensive old man, most of the jokes about whom revolved around his senility and physical frailty. In other words, yet another victim of the terrible case of Flanderization which has plagued the series. Burns also showed a very dynamic sympathetic side, where he's almost a Scrooge like figure feeling the effects of a plentiful...but empty life. This is still shown occasionally but in a lighter manner.
This trope is invoked in-universe in the Halloween special's A Nightmare on Elm Street parody. After Groundskeeper Willie (in the Freddy Krueger role) is defeated, Bart and Lisa contemplate his return. He appears moments later, but has been reduced to an ineffectual villain whose buffoonery is even accompanied by jaunty music.
Cobra Commander, the main villain of G.I. Joe, follows other aforementioned 80s cartoon villains' example but he's worth special mention because in parallel to his bumbling persona in the cartoon, his original comic book persona remained a ruthless Magnificent Bastard all throughout to its final issues. This decay was probably intentional because his bloodthirsty ways needed to be toned down for the Sunbow series. Though also worth mention is that while the cartoon Commander was mostly inept by the end of G.I. Joe's second season, at least he was a part of the sub-plot concerning an internal civil war within Cobra where Commander and a few others made up the secret sub-group Coil in an effort to slowly wrestle control of Cobra away from Cobra emperor Serpentor, giving the villain at least some credibility by the end. However in the animated movie, Coil is never mentioned and Cobra Commander goes beyond becoming everyone's Butt Monkey for the film in a literal sense, in a way decaying the character in two different ways. Fans of G.I. Joe tend to not like the movie very much based on this, and the fact the movie attempts to retcon what is known about the Commander's past to something beyond ludicrous…even by 80s cartoon standards.
On Codename: Kids Next Door, it took an age-ified Nigel and the rest of the team to take Father down in his first appearance ("Operation: G.R.O.W.-U.P.). Then a few cadets took him down in his next appearance ("Operation: T.R.A.I.N.I.N.G."), making him more of a comic-relief pest. Then the writers escalated his crimes by turning the KND into animals ("Operation: G.R.A.D.U.A.T.E.S."), and after that was taken care of, they had him extend school hours to 8:25 p.m. (a big deal, since the protagonists are school-hating children — "Operation: P.R.E.S.I.D.E.N.T."). In Operation: Z.E.R.O., he is reduced to being completely ineffectual when faced with his father. Z.E.R.O. plays with this, however: after his father banishes him for not being competent enough, he goes into a state of depression which takes his moral opposite brother to pull him out of. Together they face their father and though Father is still afraid he tries to stand up for himself. Soon after he gets sucker punched and Grandfather begins to rag on him a bit and sets off his Berserk Button. His unstoppable rage is so fierce that it makes his heroic brother, who was previously shown to not be afraid of anything, step back and makes Grandfather, the unstoppable evil who has conquered the world, afraid. But before he can do anything he gives up because he's too depressed. This shows that it's not the lack of ability that holds him back but rather the lack of self-confidence.
Speed Racer: The Next Generation had Zile Zazic, the main villain of the show, oil tycoon and trustee of the Racer Academy...who went through every possible process in which decaying villains could go through! It didn't help that he only carried out his plans first-hand two-thirds of the way through the season. By the end of the show, his plans became boring and predictable.
Jack Spicer became full-on comic relief with the emergence of Chase Young (even achieving memetic status for his lameness in-universe). Chase himself became less of a threat to the Xiaolin monks when Hannibal Roy Bean was released, moving more into Eviler Than Thou and Enemy Mine plots against Bean, but he is still an Empowered Badass NormalMagnificent Bastard to the end.
Wuya too. Starting off as a fairly credible mentor to Jack, she eventually regained her magical power and managed to take over the world off-screen. Upon her return in the second season however, she was reduced to nothing but a loud, obnoxious whiner, and by the end of the season she was reduced to being nothing more than a cheering fangirl for Chase Young. She regained some of her villainous grativas in the third season, but even then, she was just never as cool as she was in the In the Flesh 3-parter.
Valmont in Jackie Chan Adventures. Just look at the guy. In the early seasons, he was a charismatic, refined, rich-out-his-ass leader of a worldwide criminal organization who could very well be mistaken for a Magnificent Bastard (He was even able to hold his own against (and get the better of) Jackie in their personal confrontations.) Then take a gander at the later seasons...knocking over convenience stores, living in an apartment no bigger than your bathroom (seriously), and leaning on the three goons he has left to pay for the bill at a pancake shop. The last time he's ever seen, in the show's final episode, he's become a bus driver.
The Dark Hand, the criminal organization in question, went with him, going from a Nebulous Evil Organization with an army of Mooks to Finn, Ratso and Chow. Until they decide to retire because, after being repeatedly beaten up by Jackie Chan and enslaved by evil sorcerers and demons with nothing but pain to show for it, they decided Being Evil Sucks.
The Shadowkhan are a good example. They were quite potent in seasons 1 and 2, but in the Oni Mask saga, they go "poof" if someone so much as trips them (though they are central to a Near Villain Victory and World Domination scheme). Also, when the Enforcers became Dark Chi Warriors, who initially could survive falling off a cliff, but towards the end of the season, couldn't survive a fall of 10 feet.
Shendu also suffers from this. Early on, he's an ominous and threatening figure, despite being stuck as a statue. During the end of the 1st season, when he's finally regained his powers, he's a vastly powerful and menacing evil dragon. During the 2nd season, however, he's beat up by his demon siblings because he lost his body and they still have their's, then gets stuck sharing Valmont's body and is largely a joke, except during the finale, and when he later returns during the finale of the 3rd season. During the series finale, however, he's stuck helping the heroes, and is largely a joke when fighting his son Drago.
Hak Fu, though less egregiously than other examples. In his season 1 apperance he completely outclassed Jackie Chan, and left Tohru in the dust. After that he became a formidable, but beatable opponent for Jackie and was suddenly an idiot who spent too long calling his attacks.
And yet, almost any episode where Rampage didn't have a major role in the plot will have him either get curb stomped or hand him The Worf Effect. Often in a really silly way.
From the Transformers Wiki, regarding the first episode of the show, re: Waspinator: "In a stark contrast to his later career, he actually proved to be a serious threat and had the advantage over the inexperienced Cheetor, pinning the young Maximal down in a canyon." Somewhere between blowing himself up with his own missiles in episode 4 and Rattrap kicking him in the nuts at the end of season 1 his true destiny came to fruition. Amazingly, in Beast Machines he suffered villain decay all over again as Thrust.
Animated on the other hand doesn't always have them as the villains. They also reverse the Took a Level in Badass the Autobots as a whole went through by having a crew that was never meant for battle with tools that had primarily non-combat purpose in mind, so it takes the whole team to take down just one or two of the armed-to-the-teeth Decepticons.
Animated started out with the Autobots requiring all hands on deck to stand a chance against any of the Decipticons but by the end of season 3, Optimus Prime is able to take on Megatron single handed.
Starscream took a level up in badassery when he first fought the Autobots and was too strong for them (making up somewhat for the stupidity he displayed earlier), but later he's largely a joke because of how he keep getting his ass kicked by Megatron. Two other Decepticons, Blitzwing and Lugnut also suffered from this. Initially they would be considered Not So Harmless Villains. They were dumb, but either of them could take all the Autobots on his own. But as time went on, they kept on getting beaten by plot devices and largely become jokes.
Galvatron was a competent and capable leader in the '86 movie, then was driven insane and became The Neidermeyer. Early on in that particular portion of his existence, he was ridiculously powerful to the point of being able to blow up small planets, but that didn't last, and before long, he was just as ineffective as Megatron, if not moreso. And let's not even talk about what happened in post-G1 series...
Even the films have done this. The Decepticons were nearly unstoppable at first, Starscream even managing to outmaneuver the Autobots and the air force in the first film — in the sequel, they get thrown around. Although the extent of decay is hard to tell since the Autobots and humans from around the globe have been fighting for two years now as a specialized task force. They're better prepared this time. Plus the fights aren't in crowded cities, so the Autobots can cut loose, especially Optimus.
The Cons performance is poor all around, sure Starscream and Brawl could do some damage, but they were defeated rather easily, as well as most of the other cons. Look at the body count: Autobots lost one guy of five, Decepticons lost five out of eight. Almost all fights with the Autobots, bar Megatron's participation, are pretty one sided. In fairness: in the first movie the Autobots get their asses handed to them by the Decepticons unless Optimus is around; it's the humans and their pesky magnesium "can kill a Decepticon in a few hits" weapons that do most of the heavy lifting in the first movie. The magnesium weapons are so effective that one human soldier is able to kill Blackout single-handed.
Transformers Prime, following tradition, hands this to Starscream (again). He went from surprisingly competent in the pilot to standard Starscream near the end of the season. And while he dealt Arcee a No-Holds-Barred Beatdown in Partners and later went rogue, it's not been entirely undone yet. Admittedly it is justified with Megatron returning and things generally not going his way. So far Megatron hasn't been hit with this (yet), clearly being the most competent of the Cons (Soundwave perhaps being the close second). If the season 2 three-part premiere and "Operation Bumblebee" are to be believed, however, Starscream is getting back on form, particularly when he killed a dozen Vehicons in a row. And then he found the Apex Armor...
Averted with Knockout. Undoubtedly the least dangerous Decepticon character by default, two seasons in and he's remained consistent with his early appearances.
The Insecticons suffered from this and Conservation of Ninjutsu. The First delivered a brutal beating to Arcee, the Second took on Megatron and pummeled him, nearly winning, both having shot them to almost no effect. All subsequent appearances have them defeated quite easier by the Autobots and Megatron, who only need to shoot them once or twice to take them down. At first it seems that their insect mode is weaker to blaster fire, but by "The New Recruit" their Robot modes to fair just as poorly.
The Commando Droids of Star Wars: The Clone Wars went from Elite Mooks in their first appearances to almost as ineffectual as their ridiculously ineffectual cousin, the B-1 Battledroid. However, this may just be a result of them appearing more often and being pitted against more Badass characters such as Jedi and veteran clone troopers - the former being One-Man Armies and the latter having enough experience to know how to deal with them. Even then, they are still a nuisance at best for those types of characters, and they are still enough of a threat for Red Shirts and those not used to fighting wars.
General Grievous's zig-zags this quite a lot. For example, early on in Season 4 he was fooled by Jar Jar, and General Tarpals managed to injure him at the cost of his own life, allowing the Gungan army to capture him. However, near the end of the same season, Grievous went up against the Nightsisters and their Army of the Dead, led by Ventress (who for most of series prior to that had looked down on Grievous as if he were barely even worth her notice), and tore them apart. The latter was one of the few examples in the entire Star Wars franchise in which the sheer overwhelming numbers of the Droid Army were used with appropriate ruthlessness.
In Star Wars Rebels, Maul has suffered greatly even though he is still a dangerous badass. In Star Wars: The Clone Wars, he was a savage fighter chessmaster who easily massacred legions of Jedi and lead his own army of Mandalorians and Nightsisters to become a dangerous threat to both the Separatists and Galactic Republic. By the events of Rebels, Maul is on the run, lost all of his followers, and relies more on manipulating the heroes to achieve his goals. Although he is still powerful and skilled enough to take on the Imperial Inquisitiors, he admits that he is shell of his former self and quickly runs when Darth Vader. This is justified as his numerous losses to the Jedi and his brutal torture at the hands of Darth Sidious have turned him into a wreck.
Vlad was once a Magnificent Bastard and a very competent arch-foe with an often sympathetic side. But in the third season, he became a shallow crook with little redeeming qualities; his final plan was to force the world to let him save it from a giant meteor in exchange for world domination (an agenda that was poorly conceived) and 500 billion dollars...as if he wasn't already filthy stinking RICH!
Skulker is another example. In his first appearance he was genuinely menacing, and had Danny looking over his shoulder scared. Fast forward to "Micro Management", where Danny could defeat him in a few blasts, and only became a threat when Danny lost his powers. It reached its peak in "Girls Night Out", where a bird chased him off.
In his first appearance in Yin Yang Yo!, Kraggler is an incredibly elderly gargoyle who is discounted by the siblings due to his age, then proves to be a very powerful and capable villain, who, rather than being defeated, is convinced to stop because of an apology for his mistreatment. From then on, he's treated as a joke villain (even moreso than the other villains, this being a comedy series) who's only a threat if he uses magic to reduce his age.
Ra's Al Ghul himself suffered from this in Batman: The Animated Series and later DCAU canon. Introduced as the leader of a global secret society, whose first villain plan involved wiping out 99% of the human race to save the planet, and once described by Batman himself as "a criminal mastermind more dangerous than Lex Luthor and The Joker combined", Ra's would end up spending EVERY SINGLE ONE of his episodes trying out various wacky schemes to cheat death and expand his already 600 year long lifespan, instead of doing anything productive to menace the human race.
Ra's al Ghul's Villain Decay is still debatable, considering how even in the Superman: The Animated Series episode "The Demon Reborn," Batman himself declared that Ra's al Ghul was more dangerous than both The Joker and Lex Luthor combined. Later in the canon, though, they refer to something called "The Near-Apocalypse of '09," which Ra's was behind, and apparently took the whole Justice League to stop.
Ra's says in "The Demon Reborn" that he realized the Lazarus Pits effects were becoming shorter and shorter, so perhaps he was concentrating on finding out a way to live longer before trying another world domination effort.
He actually does have a couple of decent showings after that, and wasn't always portrayed as stupid; ironically, his Dumb Muscle characterization started with (and was worst in) the episode "Almost Got 'Em", the irony being "Croc" was actually Batman in disguise. Unfortunately for Croc, this was his most famous "appearance", so this is how he is remembered.
In his second appearance, while the Clock King did gain a device that actually let him control time, he also didn't show a lot of what made him such a formidable opponent in his debut episode (his ludicrously precise timing and planning). This resulted in the man who was able to physically match Batman in combat being taken out the instant his device broke. This may have been a good thing though, for those who found him able to do such a thing too hard to swallow. Fortunately he recovered from the decay in his WesternAnimation.Justice League Unlimited appearance as a member of Task Force X, in which his planning and precise timing were key to a totally successful mission by the team to steal the Annihilator from right out of the Justice League's headquarters.
Magnacat from Monster Allergy is a serious threat to the Tamers, but not anymore when his plans kept on failing, he becomes bankrupt. Hector Sinistro becomes this as well.
While never particularly smart, the Trix sisters from Winx Club were competent enemies, acting on their own in the first season. They still were more than decent during the second season, even if by then, they were already reduced to the main villain's henchwomen; notable was their fusion into a single, powerful entity in the last episode. Then the third season came, and they became little more than a joke - they even received some power-up at some point, but it turned to be useless.
Subverted at the very end of the first movie when they team up with their ancestors, the Three Ancestral Witches, promising to rip the Faeries' wings off.
Valtor eventually suffered from this at the end of season 3. Even when he was well on his way to becoming the supreme sorcerer of the Magic Dimension, he began to grow mopey and whiny about how he was always hiding and that the Trix losing to the Winx meant that his defeat at the hands of the Company of Light years before was starting to repeat himself. When the Winx managed to hit him with the Water Stars he became reluctant to even fight them. Even his demon form that removed his weakness to the water stars didn't save him, as he ended up letting the Winx free all of his spells that he had stolen, was abandoned by the Trix, and nearly frowned himself when recalling his water spell. In the end he fell under the control of the Three Ancestral Witches before being single-handedly killed by Bloom.
Tritannus gets hit with this as well, at the beginning he was real menace to the Winx along with the Trix to who he granted powers to, but he slowly starts losing to the Winx to the point that the he gets easily beaten by Selkies, who he and the Trix easily kick around.
The Hive kids started out in their first appearance as a well-organized elite fighting force that proved to be an even match for the titular heroes (even taking them down in their first encounter when they had the element of surprise), but by the last season they had decayed so badly a single Titan (Kid Flash) could trounce them all fairly easily (except for Jinx, who had a Heel–Face Turn anyways). Even when they were badass, they hardly liked each other, and weren't all that bright, save Jinx and Gizmo (who was too immature to put his brains to effective use on more than one occasion). One could argue that without Brother Blood to scare them into competence, they just really didn't care about working in tandem anymore. They probably only stuck together at all by that point because they had nowhere else to go. There's also the fact that since Teen Titans played a speedster near their full potential, Kid Flash was probably more effective alone than the main five in most cases. This is kinda re-enforced by the fact they got just one person to watch their city for the five of them.
Billy Numerous was actually somewhat competent in "Overdrive". He was able to continually thwart the Titans until he was outsmarted in the end. After that he wasn't competent anymore.
Brother Blood himself got this pretty bad. His fighting ability never really went down- it was his intelligence and ability to make effective use of his other powers that suffered. In "Deception", for example, he seems to know almost everything that's happening in the HIVE from the start (including that Cyborg was The Mole), and he was only beaten in the end because Cyborg's half-mechanical brain was able to reject him. In "Wavelength" and "Titans East", he somehow give Cyborg his own powers by mistake, is completely oblivious to when someone with no mental enhancements at all is capable of completely resisting him, and blows his top at the first opportunity. There's more to decay than just a decrease in power, after all.
In Ben 10, Clancy the bug man was a sadistic psychopath in his first appearance. When he appears in the Grand Finale, he has been turned into a generic bug monster for no reason. In fact, most of the villains that returned in the finale were decayed, with the exception of Charmcaster, who stuck to her role as Evil Counterpart to Gwen.
Even worse with the Forever Knight, who went from a mysterious evil organisation to ridiculously weak villains who served as the heroes' punching ball (to the point in one episode, Gwen felt like it was more important for Ben to assist his girlfriend's tennis match than keeping an eye on them). Fortunately corrected in season 2 of Ben 10: Ultimate Alien, where their founder comes back and turns them back into a real threat. Omniverse bring them back into this trope, since their war with the Esoterica has left them mostly decimated, with only a very small team still active.
Charmcaster may not have suffered any decay in Ben 10, but she was hit by it pretty hard in her second Alien Force appearance, where she killed Gwen of an alternate timeline and kept on boasting about it to the present Gwen...only to get her ass kicked by Gwen several times afterwards despite her claims of power. Her first appearance in Ultimate Alien then made it worse, turning her into a mook who barely held off Kevin, the team Worf, for a few minutes, and needed the help of two other bad guys to stand a chance against the heroes. Following an entry into the Heel–Face Revolving Door, however, she became a threat again, even temporarily killing the heroes at one point and from then on serving as a godlikeDimension Lord. She immediately decayed again in "Couples Retreat", in which she becomes Darkstar's wishy-washy girlfriend who barely does anything throughout the episode. This is then undone by Omniverse, where she becomes a legitimate threat again. She has permanently kicked Darkstar out of their original dimension, not to mention being super-competent when she temporarily teamed up with Ben, Rook and the gang to get back an artifact (she succeeds AND escapes, albeit with help from her Poisonous Captive Adwaita) while they were trapped on the Monster Planet Anur Transyl. She's also gained new powers, including merging with her rock monsters to form a special armor and even transforming into a dragon like Maleficent.
Zombozo initially defied this Trope in Ultimate Alien; In his original appearance, he was a horrific and creepy stalker-like character who required being a Mook Horror Show from Ghostfreak to be defeated, but was an otherwise one-shot villain. When he comes back in Ultimate Alien, he proves to be a decent, Ax-Crazy and still scary villain, forming an alliance between various villains to attempt Revenge by Proxy on Ben and almost getting Gwen's aunt killed. Sadly however, Ben 10: Omniverse decided to play this trope straight by making him Denser and Wackier and having him going for petty theft such as rob bank. He recovers from it in his final appearance.
Omniverse episode Special Delivery hits several villains with this. Most villains who show up in this episode could give a hard time to Ben in their previous appearances, and no less than three of them (Psyphon, Fisttrick and Trumbipulor) had been through impressive cases of Not-So-Harmless Villain. In this episode, they allgang up against Ben who at this point is alone and unable to call for help. Yet, he mops the floor with them. Psyphon gets slightly better on the plan of fight, but still manage to grab the Idiot Ball despite having been Dangerously Genre Savvy before.
Psyphon was hit even harder in "Bengeance is Mine", in which all his previous intelligent characterization was thrown right out the window in favor of making him Too Dumb to Live and completely reliant on Vilgax.
In Gormiti: The Lords of Nature Return, this was the fate that befell Orrore Profondo (Deep Horror), who, in the backstory narrated in the toyline, was a terrifying opponent, feared by all the Gormiti siding with the Wise Old One. He even managed to trick the Air Gormiti into doing a Face–Heel Turn...but in the series (which takes place many millennia after the toyline story), he seems to play second banana to Evil Overlord Magmion and doesn't really show the competence a villain of his caliber should. However, this only seems to apply to his anime self: in the comics, as of now, he has retained all of his credentials and Magmion is just one of his underlings.
Satan was big and scary in his first appearance in South Park, but he's become "a whiny little bitch" in God's own words ever since he was first established as the lover of Saddam Hussein. It's arguable that he started out pre-decayed, though. He LOOKED intimidating, but his master plot in his first appearance was conning the city out of a lot of betting money, rather than, you know, the End of Days or anything like that.
Ego Trip zigzags all over the place on this trope. Mandark does eventually Take Over the World as an adult, resulting in a Crapsack WorldBad Future that Dexter and a bunch of other Dexters from other points in time (including Future Badass Dexter) have to stop. However, it only happened because Mandark stole Dexter's Neurotomic Protocore. However, this happened after Dexter became a meek pencil-pusher designing cubicles as an adult, while Mandark is his rich, successful, abusive boss. And when it comes down to who will win in the end, it's all rendered moot because the day is ultimately saved by an out-of-nowhere, completely oblivious Big Damn Heroes moment by Dee Dee.
Metallo became less and less of a credible threat with each appearance. Probably intentional, too. Metallo's appearance over the episodes maintained the damage he suffered from each prior appearance, implying that he wasn't getting internal repairs, either.
Kalibak was perhaps the most obvious example. His first appearance was a whole-episode slugfest where he stood toe-to-toe with Superman. In subsequent appearances he's little more than a doorstop: Superman punches him out in less than a minute in "Legacy", and although he beat Wonder Woman he loses to Batman in Justice League. In his final appearance he finally got to do something useful... Because he was in an Enemy Mine situation with Scott Free and The Flash.
Buford was at first shown as a truly nasty bully. By the second season he's mostly just cranky and posturing and is in fact a friend of Phineas and Ferb. Also, Tri-State Unification day episode contains both of these elements. He tries to ruin the parade, but is also shown to be Vitriolic Best Buds with Baljeet, whom he used to pick on (and still does, but it's pretty blatantly out of love; he even says as much once).
Doofensmhirtz, at the beginning of the series, was a believably evil Jerk Ass who could sometimes legitimately give Perry a run for his money. Towards the end, he was stated as a Nice Guy who only pretends to be evil.
The Diesels and Spencer from Thomas the Tank Engine suffered a lot from this trope. Diesel 10 as well. In The Movie, he tried to have every single steam locomotive destroyed and ended up being thrown off a bridge and onto a barge full of sludge, but in one of the sequels he actually wants to take over the Steamworks because of the Dieselworks' poor conditions, and later trapping Thomas and Percy inside the Dieselworks and setting the entire place on fire only to end up being scolded by Sir Topham Hatt at the last minute and is forced to put out the fire he started and repair the entire Dieselworks as punishment because of this!
All villains from The Powerpuff Girls other than HIM suffered villain decay, especially Mojo Jojo, who was actually able to take over Townsville with an army of monkeys in the movie, which takes place before any other event in the series. Even Him suffered a few degrading roles in the show as well (in the writers' defense, he was an insane effeminate crossdresser, how could they resist?), as did Mojo continue having the odd threatening role however. While a lot of other villains got progressively worse, the competence for both former characters was arguably more a case of Depending on the Writer.
Hotstreak started out as the biggest bully in school and the leader of a local street gang who becomes even more dangerous when he got exposed to the big bang gas with the ability to control fire. He was a genuine threat for his first couple of appearances but as the series went on he became more and more pathetic. He was decayed so badly that on one occasion when one of the heroines gave him a wedgie he ran away crying. What is he now, Jack Spicer?
Ebon also suffers for this. He's threatening at first, but gets his ass handed to him in nearly every appearance even with help form his henchmen, and loses fights against supporting characters.
Cedric, The Dragon from W.I.T.C.H., was quite menacing and monstrous in his first few appearances. As the series went on, though, his purpose largely became to get his clock cleaned by the heroines every few episodes, quickly robbing him of any serious threat. The series finale even yanked his chain by having him become supremely powerful...only to not realize he didn't know how to properly utilize it, and he gets beaten up rather easily AGAIN. Lampshaded in the first season finale, when Phoboschewed Cedric out for his failures epically, then used his newly-heightened magic powers to curse him into a pathetically small and weak version of his One-Winged Angel form.
Wolverine and the X-Men had the Brotherhood of Mutants first appear with a relatively clever plan that framed the X-Men for an attempted assassination. As the series went on and on, however, Pietro became increasingly stupider, and the effectiveness of group decreased.
Disney originally had Captain Hook be somewhat dangerous in Peter Pan, with him being decently competent against Peter. However, by Jake And The Neverland Pirates, he is now absolutely stupid and has a small ball on the end of his hook. Maybe small children are scared by pointy hooks, but it just seems silly. Or maybe he was just so clumsy with the hook that his crew did this so he would stop tearing his face off while grooming his beard.
The Hobgoblin experiences this, being outclassed by the Green Goblin in his last appearance. The story editor John Semper hated The Hobgoblin character and only used him due to Executive Meddling (his predecessor had plans to use the Hobgoblin instead of The Green Goblin and by the time Semper replaced him the toy had been commissioned and it was too late to change plans). So no surprise he became the Green Goblin's bitch.
Doctor Octopus also suffers from this where in as the series goes he descends into being nothing more but Kingpin's lackey.
Robotnik from Sonic SatAM. Season 1 played him as a genuine threat and a serious intimidating character opposed to his usual clownish forms in other media, but Season 2 introduced a Story Arc in which his continued failures and increasing irrationality and buffoonishness start to grate on assistant Snively. His obsession with destroying Sonic also led to several moments of Bond Villain Stupidity, something he was far too wary about originally most of the time. He was far from immune to it however as even in the first episode his decent plan failed solely because he became obsessed with hitting Sonic first.
The Lieutenant, Amon's electric stick-wielding second in command from The Legend of Korra, starts out as a pretty effective villain, absolutely crushing Mako and Bolin in his first appearance and giving both Lin Beifong and Korra herself the fight of their lives in his next one. In every single episode after that, though, he rarely does much more than show up, flail around a little bit, and get launched over the horizon in short order.
Zordrak of The Dreamstone, while he always usually left the dirty work to his mooks the Urpney, he was initially presented as a calculating, reserved villain who tactized a lot of the plans and had the odd moment of physical involvement (where upon things usually got a lot darker in tone). While the second season starts off well with his discovery of the Nightmare Stone, he quickly devolves afterwards, having little role outside something of a demonic Pointy-Haired Boss for the Urpneys. Since Urpgor and Blob's team were now required to concoct plans themselves, this did lead to a mild subversion in their case however.
Dark Vegan was introduced as someone who could wipe out all life on Earth, and already had done so on multiple other planets, but by his third appearance he had decayed to the point where Johnny frequently thwarted him without even knowing he was there, and is more of a wacky nextdoor neighbor than a real villain. It's explained that he's stuck on Earth, and as a result is without his army or the ability to replace his damaged weapons.
Eugene aka "Bling Boy Boy", who started as Johnny's Arch-Enemy but devolved into a frequent Anti-Hero friend of his.
Liquidator from Darkwing Duck. In his first appearance he had a lot of water-based powers, but seemed to lose them after that. (In fact, he didn't even appear as a villain by himself in subsequent episodes, only appearing as a member of the Fearsome Five.) This is probably because not only was he way too powerful to be a recurring enemy to a Badass Normal, but there were only a handful of ways he could be truly beaten.
The series invokes it in the Ice King for Character Development. IK was the Big Bad at the beginning of the series (although he was a bit of an ineffectualwoobie even then), but his character becomes increasingly tragic and sympathetic as his origin and former self were revealed. As the heroes grow to realize this, they begin to treat him with less animosity, and in turn he mellows out. By now, he's more an annoyance than a threat.
The show tries its hardest avert this trope with the Lich by having him show up only in big season finales—the less he shows up, the less we have to see him being beaten. But even with only three real appearances to date, his impact has decayed just slightly enough that the writers decided to temporarily shelve the character by having Finn turn him into a harmless giant baby. Ironically, this might be the ultimate example of villain decay, if it weren't made clear that the Lich we know and fear is still alive somewhere in there. For the next major finale in Season 6, a substitute villain is introduced, more comedic but just as threatening.
Discord is introduced as a genuine threat that even Princess Celestia is afraid of, whose danger is limited only by his lack of ambition. In Season Three, however, he's deliberately released by Celestia to be reformed, and spends the episode hanging out in Fluttershy's house and having a dinner party with the ponies, being merely a Jerkass the whole time. Interestingly, he's every bit as powerful as he was before, and he's only pretending to be reformed so he can screw around with the ponies. However, ultimately, Discord comes to consider Fluttershy a friend and makes a Heel–Face Turn for her sake. The decay goes even further in seasons 4 and 5, where Discord is reduced to a "reality bending comic relief" type of character, and his role in the show mostly boils down to being a clingy, jealous brat trying to spoil others' fun whenever he doesn't feel he gets enough attention. Lampshaded by Tirek during the Season 4 finale.
In the toyline, the talking Nightmare Moon toy got hit with this. Despite her name and voice, none of her lines (apart from an Evil Laugh) sound like something a villain would say.
My star barrettes are fabulous!
Tuma, his Rock Tribe and the Bone Hunters in BIONICLE: The Legend Reborn are virtually wholly separate entities from their depiction in the preceding stories — Tuma goes from an intelligent warlord Big Bad to a bumbling underling, and his tribe from an army of unbeatable warriors to goofy one-hit-kill Mooks... that couldn't even talk! The Bone Hunters received the same treatment, even though a single group of them could only barely be defeated in an earlier book. In a meta-sense, this is actually an inversion — the movie was written first, and the rest of the story material later. External sources did justify some of this threat decay better than the movie, though.
Heather is a justified case. While she was able to cheat and manipulate her way through the first season, she became pretty harmless in Total Drama Action due to nobody trusting her. As such, she didn't do much that season outside of cry over losing her hair. She's still a danger to the other contestants, but she's nowhere near as bad as she used to be.
The Royal Flush Gang in Batman Beyond was at their best in their first episode. In the second, they shoot themselves in the foot by alienating Melanie/Ten with their scheme. In their third and final appearance, they're on their last legs. King and Queen's relationship is falling apart as Queen constantly compares King negatively to her father the previous King, Ace is literally falling apart since they can no longer afford reliable repairs, and Jack ends up in prison by the midpoint of the episode. Batman barely has to do anything to beat them this time. They pretty much defeat themselves.
Batman's entire rogues gallery eventually suffers from this in The Batman, with the exception of Hugo Strange and possibly Catwoman. In one of the later episodes of the series, Batman and Robin manage to take on and defeat literally all of them (minus Strange and Catwoman) in a couple of minutes and with no injuries at all. While it's arguable that some of this was due to their poor/nonexistent teamwork, it still looks pretty bad.
As Season 1 unfolded and Hater revealed himself to be more of a misdirected, lovable goof and not really a REAL bad guy, we knew that we had to introduce a serious and legit villain to shake things up and throw our whole goofy show back on its heels... After a whole season of having Wander handily defeat/befriend Lord Hater at every turn, it became hard to take him seriously as a credible threat.
While Gideon, Big Bad of the first season of Gravity Falls averted it in his first re-appearance in Season 2, "The Stanchurian Candidate", it was then played straight with him in "Weirdmageddon Part 1", where he is just a flunky to the true Big Bad Bill Cipher, and his usual creepiness is completely absent in favor of the pure comedy of him being a stereotypical Corrupt Hick sheriff (as Wendy puts it: "He's gotten folksier!"). Genuinely caring about his fellow prison inmate gang members also neuters his villainy. In the end, his Heel–Face Turn doesn't come off as too surprising as a result.
In Steven Universe, Peridot, the show's first real villain, was introduced as a coldly emotionless and calculating agent of the Gem Homeworld, at one point crushing one of her robots underfoot because it had sustained damage. Half a season later, after being trapped on Earth, stripped of her vehicles and robots, defeated regularly and losing a foot, she's reduced to abducting Steven in the hope his healing powers can fix the Homeworld Warp panel and get her off this rock. And shortly after that, she's poofed, loses her prosthetics - leaving her the size of a ten-year-old - and her schemes are reduced to locking herself in Steven's bathroom and refusing to come out, then offering an Enemy Mine since it's the only way to preserve her own skin. Spending time with Steven and the Crystal Gems brings about a Heel–Face Turn after failing to reason with Yellow Diamond to save the Earth.
In Generator Rex, No-Face was one of Rex's most powerful enemies. When the city of Kiev is quarantined to hold off some of the most powerful EVOs, No-Face emerges as their leader. Powerful and utterly insane, No-Face defeats both Rex and Six in his debut episode, and in his second appearance he beat Rex within an inch of his life and even took on Van Kleiss, the Big Bad, for daring to suggest that Rex was needed alive. Come his third appearance he's been captured offscreen, and easily put into a full-nelson by Hunter Cain, by and large a normal human, before joining up with Rex's C-listers. This time, Rex curb stomps him twice, and when the opportunity to kill him arrises, Cain's able to threaten No-Face to back off.