Magical Project S Pixy Misa starts every episode ruining the balance of good vs evil (that's her purpose) but ends acting for the Evulz and more often than not ends vacationing (justified in that she is not actually evil but she just represents the repressed aspects of Misao and doesn't really care for her goals) instead of torturing Sammy and in one episode she ended having vacations instead of destroying Sammy.
Pokémon: Brock's life goal was to be a great Pokémon breeder. You'd never know it nowadays. He finally left the show becoming a Pokémon doctor.
Misty wanted Ash to repay/replace the bike he inadvertently trashed in the first episode, which is why she followed him around so much. Near the end of the first season, we find out that she actually forgot about the bike, and begins hounding Ash about it when he accidently reminds her. Her bike was repaired before she left the show for May. Then again, soon after she first starts following Ash around she's doing so from behind trees, hastily mentioning her bike when she's found out. It seems to imply that she does like hanging around Ash but doesn't want to admit it so she uses the bike as an excuse so it makes sense that she'd occasionally completely forget about it.
That nearly-forgotten motive's referenced in the DVD commentary for the English version of the first movie. The director relates that, while they were trying to come up with an appropriate two-syllable translation for Misty's horrified reaction to Ash's apparent death, Misty's voice actress Rachel Lillis ad-libbed "my bike!"
Also, Ash's goal was To Be a Master; that is, to become the world's greatest Pokémon Master (a Pokémon Master being a trainer who is an official part of the Pokémon League). Nowadays, this goal is barely referenced, and Ash seems to be going around fighting Pokémon battles for the heck of it. In Season 9, he was even offered the position of Frontier Brain, which would make him a Pokémon Master, but he turned it down.
We actually don't know if it would have made him a master. The definition has never been clearly defined.
His goal seems to be to be the grand champion of a major region (Orange Islands doesn't count, apparently). Then again, Ash seems more interested in the journey than the destination; he takes no shortcuts getting there and prefers to just travel the land instead of settling into some position of power. It's likely that "To Be a Master" was just an excuse from the start... Or it's his retirement plan.
The Team Rocket trio, who originally decided to follow Ash because his Pikachu blew up a Pokémon Center. Since they were trying to steal strong Pokémon, this made sense. Through the show's run, however, we have encountered numerous Pokémon who are significantly more powerful than Pikachu. They continue (on and off) to attempt to get Pikachu because they refuse to give up, even though their boss never cared about Pikachu in the first place.
This sort of thing happened across international lines as part of 4Kids Entertainment's dub of Yu-Gi-Oh!. They usually played down the sympathy-inducing backstories of the villains and made them more evil. Pegasus' goal was the same (to bring back his lover Cecilia) but the methods were more ruthless. In the original, he needed to defeat Yugi so that he could gain control of Kaibacorp's technology and create a hologram of Cecilia to live with. In the dub, he wanted Yugi's Millennium Puzzle and all Millennium Items so that he could bring Cecilia's soul back and infuse it into the hologram. It's said in the dub that in doing so, he could inadvertently destroy the world. Although probably unintentional, this motive shift actually makes sense in the long run, as the seven items together DO open the door to the afterlife (where Pegasus could get Cecilia's soul) and also unleash the power of Zorc Necrophades into the world, which could indeed destroy it against Pegasus's wishes (this is Yami Bakura's intentional goal.)
Marik/Malik got it worse, though. In the original, he simply wanted to escape the life of a tomb keeper, kill Yugi (more specifically, the pharaoh), whom he believed had killed his father, and live peacefully ever after with his sister and stepbrother. In the dub, this is changed to him wanting Yugi's Millennium Puzzle and the God Cards to rule the world "as pharaoh". It's even worse with Yami Marik, who, in the original, was essentially the Joker with ancient Egyptian shadow magic. In the dub, he wants to rule the world, too.
Meanwhile dark Bakura suffered this in-universe for a while, retroactively. He turns out to have had fairlygood reasons for messing with the royal family, at one point, which somehow became a plan to destroy either Egypt or the world, partly because the spirit of hatred born from the slaughter of his family (Japanese) or an ancient primal destructive dark thing (English) teamed up with him. He seems to have entered the series with amnesia, carrying him still farther from sanity. But he gets back to the revenge-and-end-of-world thing in the Millenium World arc.
Divine of Yu-Gi-Oh! 5Ds starts out as some sort of Visionary Villain, being the leader of a movement giving shelter to the repudiated Psychic Duelists, wanting to form an army with them to take revenge on all the people hating and shunning them, making the world a better place for Psychic Duelists. Though his plans got foiled by his sudden death. But miraculously he returned and Character Derailment did take the best of him. While he was always close to the Moral Event Horizon, but also had his goals and clearly shared more with Aki than just mind control, he suddenly forgot all about his earlier intentions, turned into a psychopathic dumbass, causing his own death with the most ridiculous Engineered Public Confession and got eaten by a giant frog just in time to exculpate Aki from all guilt and before he was about to kill the main character.
Divine is subject to a bit of Alternate Character Interpretation, on account of the fact that he's such a Manipulative Bastard that it's hard to discern where his facade of geniality ends and his actual feelings begin. Does he truly care for Aki on some level, or is he just using false kindness to make her more and more emotionally dependent on him? Is his goal really to demand societal acceptance of psychic duelists and take revenge on those who shunned them, or is he just raising a personal army of Tykebombs to do his bidding? Is he merely ruthless in pursuit of his goals, or is he an outright sociopath? Depending on how the individual viewer answers these questions, it's arguable that in his reappearance after his apparent death, he hasn't undergone Motive Decay but has simply dropped all pretenses.
Must have been a lot of pretense and especially braincells to drop if he was intelligent enough to hide all those evil motives and sociopathy during the first one and a half arc, but all of a sudden completely forgot better not to insult the owner of a Jibakushin, which was in the near vicinity to boot.
Naraku from InuYasha has changed motives so many times that eventually he was evil just for the sake of being evil. Initially, he wanted to use the Shikon no Tama to become a powerful full-fledged youkai, so his goal is getting all the shards of the Jewel. But then, he was somewhat driven by his lust for Kikyo and hatred for Inuyasha, both coming from his human heart, so his goal becomes getting rid of that. He succeeds in separating his physical heart and discarding his feelings for Kikyou, so now his goal changes to killing her. But it turns out he needs both his heart and feelings to do this so the goal becomes reabsorbing them, and when he does, he finally kills her. In the end, he succeeds in getting the whole Shikon Jewel, but he neither absorbs it nor does he wish on it, he just decides to use it to kill his enemies. Naraku himself admits he's not sure what comes next after he's done that. Yes, that's right - he spends over 500 issues of the manga trying to get the jewel, and once he finally has it, he's not sure what to do with it. Even worse, it's revealed later that he did make a wish on the Jewel but was not granted: to have Kikyou's heart. One of the reasons for him changing his mind so often is that Naraku is really a collective entity of many Youkai and a human man called Onigumo, and spends much of his time attempting (and succeeding) at absorbing other youkai into itself, so it is reasonable to expect his personality and goals to change to a significant degree (it has even been a plot point on occasion), but to also be contradictory especially when it comes to Kikyou and the Jewel, since the youkai hate her but Onigumo "loves" her, and the youkai want the Jewel to become powerful and Onigumo wants it to have her. This is lampshaded when Naraku first separated his human heart (and thus Onigumo) from his body. Onigumo angrily complained that after selling his soul to the youkai, nothing went the way he had expected.
Orochimaru's experiments and his usage of different bodies from ninja, started as a method to learn every jutsu and gain immortality. However, his continuous experiments in the Cursed Seal seem not to do that and turn them into monstrous beings, not really related to his original goal. Sasuke actually called him out on this before finishing him.
Inverted with Sasuke. His goals have always remained more or less the same: kill his brother, Itachi, and restore his clan, but how he plans to accomplish these goals has begun to vary wildly as the deterioration of Sasuke's mental state has become more rapid. After Itachi's death, his goals switched from killing Konoha's elders, to killing Danzo, to destroying Konoha, to killing every last man, woman and child in Konoha because he believes they're laughing at him over the unprovoked destruction of his clan.
Jerid Messa from Zeta Gundam starts off as an ambitious elite soldier (by mediocre Federation standards), and has the goal of one day leading the Titans forces, even if the only reason is for the power that such a position would provide. A number of situations in the series even make him a relatively good guy in everyday life. After one too many fights with the series protagonist, he has transformed into an individual completely focused on nothing but pure bloody vengeance.
To be fair, his breakdown is largely precipitated by the death of his love interest Maua Pharaoh. Who was one of the more decent characters in the series. While she's on the "bad guys'" side, she's never shown to do anything morally reprehensible herself, which is saying something in a series where even a good number of the "good guys" former nazi-expys with questionable motives and war crimes on their rap sheets.
Same for Mashymere Cello in Gundam ZZ. Captain of a Neo Zeon ship, very idealistic and unwilling to authorize actions that would endanger civilians. Tries to keep his cool and conduct battles in a way that would make Haman Karn proud of him. Ducks out early on after it's decided he's not up to the task of defeating the hero... only to come back later on as a cold and merciless soldier. In an aversion though, the final battle still shows him as the lesser of two evils due to an Enemy Civil War, and he gets to go out in a blaze of glory.
This is a side effect of having even more CyberNewtype enhancements. Best case scenario, the enhanced person goes a little nutty. Worse case scenario, they become raving lunatics bent on causing as much property damage as possible. Mashimar tends toward the latter.
Blue Cosmos from Gundam SEED suffers greatly from this trope. Originally they were an environmental pressure group, but after Human genetic enhancement became possible they shifted their focus to preventing widespread genetic modification. After genetic enhancement did become widespread they became a militant/terrorist organization bent on killing anyone who had their DNA altered. When war finally breaks out between the genetically enhanced Coordinators and the natural humans of Earth Blue Cosmos begins artificially enhancing their own people to fight one on one with the Coordinators. Then it all turns out they were just a catspaw to Logos who do it for profit.
Suzaku Kururugi in Code Geass starts off as a heroic upstanding fellow, who wants to change the system from the inside. After the death of Euphemia at the hands of Lelouch, he more or less seems to go temporarily insane, leading to a justified battle with the Magnificent Bastard Protagonist Lelouch. However, in the interim between both seasons going well into R2, not only has he become a Jerkass of ridiculous proportions, he has sold out his old best friend for a step up the power ladder, and his goal of changing the system from within has degraded to making his own homeland a better place (effectively giving the rest of the enslaved Areas of Britannia the middle finger). He does eventually realize that prioritizing means over ends really doesn't pay off after a couple of My God, What Have I Done? moments and proceeds to team up with Lelouch to save the world and atone for his sins.
The Black Knights undergo a similar one in R2 19 when they intend to sell out Lelouch to Schneizel in exchange for Japan, at the expense the rest of the world represented by UFN, for which the B Ks made up the primary military force, and their fight against Britannia's dominion of the world, and there was no actual guarantee that Britannia would keep their hands off of Japan once and for all. (And their own ally Kallen was nearly caught in the crossfire.) None of this went very far at all, given that Lelouch was whisked away by Rolo in a Heroic Sacrifice the moment things started to go south, and Xingke and Kaguya would soon catch Ohgi trying to cover the whole thing up.
After the aforementioned event in addition to Nunnally's apparent demise, Lelouch, who prior to the betrayal had actually assembled a legitimate front in the UFN to battle Britannia, now decides to go it alone, abandoning all personal inhibitions and willing to use his geass on anyone and go to even more drastic extremes, including making FacelessSlave Mooks out of his new army, detonating the world's biggest energy reserve and apparently causing more death and destruction than he did during his rebellion pre-betrayal. The latter (or former technically) was at least somewhat justified because of the opposition he faced off against. It's not that he became evil per se; the plot justifies it as him centering the world's hate around him for world peace. However, given the leading circumstances and the plausibility of such a plan (and Lelouch's own admission that it was a gamble), it all seemed like a convenient death wish for him. The aforementioned fact that causing worse, unnecessitated destruction was a path to atonement, even as a mask, when it is even noted in side materials by Lelouch that there are other methods, makes it seem more a case of Designated than Necessarily Evil.
Charles being a Well-Intentioned Extremist reveals him to be worse than Lelouch and Suzaku combined in this regard. He conquered most of the world just to take control of the Thought Elevators scattered around the globe, allowing him to get to the World of C to destroy "God" and kill free will itself.
Asuham Boone in Overman King Gainer wants revenge on Gain for his sister, but is an overall good guy. Eventually his obsession as Gain continues leading the Yapan people to Yapan leads him to decide to freeze the world using the Overdevil. Its eventually revealed that Asuham's sister had a one night stand and Asuham overreacted.
Roy Mustang starts out trying to become the best damn leader in the world, but it starts to go wrong when he faces Envy, who killed Hughes. Fortunately, Hawkeye helps him out. With death threats.
A better example would be the Big Bad — he originally started out as a lab experiment who couldn't survive outside of the tiny flask it was created in, and caused the end of an ancient civilization to gain a human body of its own. After that, it starts an elaborate Ancient Conspiracy, sealing itself in a dark underground hideout, preparing for the day it can absorb God. Van Hohenheim even points out that it's essentially back where it started.
Haru, The Hero of Rave Master, had a pretty easy motive "I want to save the world". He keeps it up for all 35 volumes. It's the Big Bad, Lucia, who can't seem to decide what his reason for fighting is (lampshaded once). When he first appears he claims to simply be after power, then he wants to prove his family isn't crazy (by taking over the world), then he wants to be a god, then he wants power again, then he wants to break some curse that was put on his family for stopping humans from going extinct by making them all die after all.
Toward the end of Speed Grapher, someone with the people skills and political savvy to become Prime Minister becomes an all-consuming openly megalomaniacal beast with nothing more important to do than indulge in evil laughter and pull grotesque faces. What makes this Egregious is that before he appeared to have a plan with substantially evil implications on the lives of real people, but that all degenerates into Bond Villain Stupidity just to terrorize a little girl he claims to worship.