The very first Digimon Adventure The Monster of the Week for the first few episodes - Kuwagamon, Shellmon and Seadramon - aren't tainted by any sort of evil magic or science, and don't speak, which is very unlike most antagonist Digimon from the rest of the show.
This was particularly a problem for the English dub, which was being produced at almost the same time as the original, which led to mentions in the early episodes of Mimi's non-existent brother, Tai and Kari's non-existent puppy, and Matt and T.K. being half-brothers despite having the same mother and father.
Digimon In general. In the earliest adaptations, including first ever appearance in C'mon Digimon, human partners could not make their monsters evolve at will, evolutionary levels were a lot less important over all, quite a few Digimon characters actually had names and monsters rarely called attacks. And monster was the preferred short hand human characters used for Digital Monsters rather than Digimon. The art style has shifted too, though that is not as noticeable since designs have rarely been upgraded after C-mon.
YuYu Hakusho had early chapters (as well as early episodes) involve him solving cases involving demons from the Spirit World (the manga even more so as a good chunk of the early chapters were nothing but Yuusuke floating around the afterlife trying to do some good deeds; in the making of the anime, they even skipped whole volumes of this. Impressive, considering the near lack of filler). By the time the Toguro brothers were introduced, it became more focused on his combat abilities and strengths fighting demons rather than solving cases.
The very first scene of Tengen Toppa Gurren Lagann is clearly supposed to be foreshadowing a scene from later in the series... Except, that scene never ends up happening. Even to a long-time viewer of the show, it makes very little sense and doesn't gel that well with how the story lays out. It's clear that at this point, only a loose version of the complete story was ready.
Fans were eventually handed an explanation when one fan asked if it was an alternate continuity where the Spiral Nemisis happened. The response? "Sure, let's go with that."
The first few volumes (and episodes) of Bleach were primarily a Monster of the Week storyline. Then the Soul Reapers got introduced, and the plot shifted gears, eventually leading to an all out war.
A character-specific example is Mayuri Kurotsuchi, originally an Ax-Crazy, bloodthirsty Mad Scientist. After his escape from his battle with Ishida (whose grandfather he killed), he's for the most part changed to being a comically sadistic character instead of the horrifying villain he was introduced as.
Mahou Sensei Negima! was originally a Harem Series... for all of two volumes. After that, more and more shounen elements were added, to the point that other than having some of the same characters, some of the most recent chapters look like they're from a completely different series. Pretty much everything from volume 10 or so onward is a straight action manga with comedic and harem elements. If you compare Negi's early flaws (timid, gets scared and runs away) with his later ones (aggressive, too solitary) the contrast is very sharp and can't entirely be chalked up to character development.
This was actually done intentionally by the author, interestingly enough, as 'the shift that occurs roughly during the third or fourth volume was a sneaky method of getting past some Executive Meddling: Ken Akamatsu wanted to do a straight-up Shōnen fighting series, whereas his editors wanted him to do another Harem comedy due to the success of his previous manga, Love Hina. The shift at first is subtle enough to work.
The first season of Magical Girl Lyrical Nanoha, particularly its first episodes. Even ignoring the constant Genre Shift of the franchise, there are several elements that are out of place now that the series has several rules set. For example, Devices apparently needed a long incantation to unlock (Nanoha being able to do it with a simple "Please" was shown to be special) and they were apparently shapeshifting weapons that could become whatever its owner imagined them to be. These two features were quietly discarded after the first three episodes and never mentioned again.
Heck, Yuuno's mere existence is one, being a mage who isn't a familiar that became a ferret when his Mana was low, a trait unique to him in the setting after four/five seasons. The latest explanation at the start of Sequence 1-1 (i.e. Chapter 5) of The MovieManga was that the Earth's magical field was incompatible with him, turning him into a ferret after he ran out of energy.
The series title is a leftover of this trope. Early on, an episode revealed that "Lyrical" was suposed to be Nanoha's special magic word that gave her more power. It's never mentioned again. Ever.
For its first story arc, Dragon Ball was an updated retelling of Journey to the West with a few vague science-fiction elements. When it came to the Tenkaichi Budoukai story arc immediately thereafter, it jumped feet-first into martial arts action, and when the Red Ribbon Army was introduced immediately after THAT, the world became openly, and proudly, Fantasy Kitchen Sink for the rest of the series's run.
If one considers the entirety of the continuum, Dragon Ball acts as a series long Weirdness to Dragon Ball Z. The moment Raditz showed up and opened Earth to the galaxy was the point when the theme and story shifted heavily. It's no wonder the anime made them separate series.
One element early on in the series that really sees some head-scratching is the conclusion of the Boss Rabbit storyline. Considering it ends with Goku actually going into outer space with no space suit and dropping the villains of it off onto the moon, it always feels weird seeing climax of the Frieza Saga where Goku has to escape the dying Namek in time, since if the explosion doesn't kill him then the vacuum of outer space will.
In the first five or so volumes of Oh My Goddess!, Keiichi wasn't as shy around women (though he was still squeamish), seemed like more of a plain Unlucky Everydude than a mistreated Nice Guy, and Belldandy seemed to know more about Earth than her anime adaptations, was quick-witted, and dressed in an elaborate Oriental-style robe. The series began as basically a college-student drama with a goddess in it (later two, when Urd showed up, and three, when Skuld appeared). After the Lord of Terror Arc, and began to resemble more of a cross between a Dom Com and a Fantastic Comedy.
Belldandy didn't just seem to know more about Earth, there were various implications that she was a bit of a Bitch in Sheep's Clothing and was subtly tormenting Keiichi in revenge for his getting her stuck on Earth. This was obviously dropped in favor of her being Incorruptible Pure Pureness incarnate (to the point that shackling a demon to her turned the demon into an angel). Urd was also much more heavily implied to be an Anything That Moves vamp at the start, which settled down into her being just sensual. About the only one whose characterization isn't hit with this is Skuld, who showed up after the series began to really gel.
While Pikachu eventually came around, he initally thought that Ash would get him killed. Pikachu would shock Ash deliberately when upset, until at least Celadon City. Now, they're inseparable.
The 9th episode, The School of Hard Knocks has two ideas that were dropped right afterwards. It was the only episode to reference numbered Character Levels (as in the RPG game mechanics) and it was the only one where Ash showed a crush on a female character (despite now being the ultimate Chaste Hero). Some fans still assume that these elements were still true- despite the episode being made nearly 14 years ago and not mentionedsince. This is also one of the rare moments where Brock has shown attraction to a girl around Ash's age. Typically he shows attraction to women or to girls in their later teens. The other was Casey of all characters, where in the Japanese version she said she'd be fun in eight years. Both were in Original Series episodes.
Early chapters of Pokémon Special has some of this, likely by the mangaka trying to figure which game elements he wanted to use in his stories. In the RGB arc, there was no Ground immunity to Electric, it was claimed that there were only 150 Pokémon (and Mew), there was one instance of non-Pokemon animals, HMs and TMs existed, and it was also quite violent at parts (Red was once attacked by zombie Pokemon one of which was dissolved by acid, and Blue/Green seemingly has his Charmeleon kill Koga's Arbok by cutting it in half). Things got smoothed out a bit in later arcs.
Early Pokémon manga in general. Nowadays they're almost always Shōnen based directly on the games, or sometimes with original characters. Older ones had more variety. They included Gross Out Shows, 4Koma with odd jokes, Slice of Life, and series that ventured away from the typical "Battle Pokémon, Win Badges, Be a Hot-Blooded Kid" outline so common within the franchise.
Compare the Kanto league saga, which only took around 80 episodes to complete, to later game-based league sagas. For one, the only Gym Leader of the Kanto League to dress like his game counterpart was Koga.
A few early Gym Leaders gave Ash their badges for helping them out in different ways, even though he didn't officially defeat them (the Cerulean and Celadon Gym Battles were interrupted by Team Rocket and a fire respectively, and the Haunter that Ash led back to the Saffron Gym snapped Sabrina out of her Creepy Child persona)— starting with Koga, no other leaders have made exceptions like these. This was lampshaded at the Cinnabar Gym, when Ash expects to receive his badge, but Blaine only intended to let him re-challenge him for it.
Emphasis on Rule of Funny also led to some bizarre situations, like a talking Gastly which godmoded by conjuring up illusions (rather than using typical moves) to counter any Pokémon attack.
There was also the Pokédex, who is usually just a computer spouting off information about Pokémon. In the first episode, it seemed to have a personality as a Deadpan Snarker, acting like a dick toward Ash when he found a Rattata going through his bag.
The Kanto and Johto episodes of the anime were a lot more Japanese than you see in Hoenn or Sinnoh. Unova and Kalos are justified since they're based heavily on America and France.
In the earlier seasons characters, especially gym leaders, barely resembled their game counterparts in terms of personality. Kanto even changed their designs, while other seasons kept them a lot truer. At least one of these changes - Misty being tsundere - was added to the games to a lesser degree.. Still there's something odd in Shrinking Violet Jasmine becoming a loud, boisterous woman. Her reappearance in Sinnoh didn't attempt to tone her down much and to make it weirder in her first episode she was closer to the games.
Sailor Moon wore a mask in the beginning of her series, when she was a much more clear-cut Expy of Sailor V.
Yami Yugi's appearance came off extremely sinister in early chapters of the manga. Gradually his appearance shifted so that he just looks like a more confident version of Yugi by the end of the first volume. The first couple of chapters, however, he looked downright psychotic.
The English Dub is infamous for cutting out all references to or hints of death or violence, but surprisingly was a bit more lenient on it in the earlier episodes, especially during Yami Yugi's duel with Panik where Panik attempting to light Yugi on fire if Yugi loses, amazingly enough, is left intact.
The Land of Waves Arc has much more realistic and 'gritty' feel than the main plot, the Non-Action Big Bad being a sharp suited shipping magnate trying to prevent a bridge being built to an island village so he can continue exploiting its inhabitants and the ninjas being mercenaries doing a job - in fact, it is the only storyline focusing on the ninjas' role as assassins. The technology base also seems to be closer to our world - there is a caterpillar-tracked crane shown in the building scenes, and one panel even shows a gun behind a shop counter.
Might Guy summons Ningame, a ninja turtle, in his first appearance. This is odd because Guy would pretty quickly establish he fights purely with taijutsu, and nothing else outside the databooks would indicate he was even capable of either ninjutsu or genjutsu. Ningame does get summoned once again years later in a rather funny scene that lampshades the whole bit.
The first English dubbed episode of InuYasha involved a fair amount of Ye Olde Butcherede Englishe from villagers and Kaede. By the following episode, it was entirely absent aside from Kaede's "ye". Considering how horribly forced one villager's reading of a particularly convoluted line was, this was a blessing.
Most of the weirdness in Slayers is two-fold: It began as a self-aware parody of fantasy series, albeit with its own dogma. As soon as the story began to emerge some time in the middle, the self-awareness angle was dropped. Also, earlier, the characters were far more cooperative with one another, and whatever new magic showed up garnered an explanation for the viewers. Newer seasons had a lot more friction (to the point that Zelgadis would continually try to run away) and dropped explanations.
In the first anime season, the four Filler episodes that were meant for comedy actually are a part of the plot - and mixed in a way that was done very well (all four episodes involve a humorous incident occurring during what is basically a bounty hunter chasing the protagonists). The second season fillers were only marginally related to the plot, and then by the third, they became more like the standard trope.
This happens in the novels as well; the first story arc is one long narrative, the second is more episodic.
Early in the manga version of Urusei Yatsura, Ataru was the only main character, rather than sharing that status with Lum (chapter 2 didn't feature Lum at all)note Originally, Takahashi had conceived of the series as an anthology series, with Ataru running into a different group of "obnoxious aliens" each installment. It was only that Lum became instantly popular that Takahashi did an immediate retool of the concept. In the game of tag in the first chapter, Lum isn't shown to have her electrical-shock ability, unlike in the anime adaptation. There were also many examples of Art Evolution (Cherry was drawn taller than usual, male characters had Big Ol' Eyebrows, eyes were drawn more realistically and less tall-and-narrow, etc.) Lum was also much more ambiguously antagonistic and perhaps even malevolent at the beginning, as opposed to the sweet naif that she became later on. For instance, in an early installment, Lum continually lies that she is pregnant by Ataru, both to wind up Rei (a shapechanging member of her race who was once engaged to Lum and is intensely jealous) and to twist the dagger in Shinobu... and Lum is clearly deriving pleasure from the chaos she is sowing. The Lum from even a year later would not do things like this.
The "Ataru is supposed to be the only main character" and Lum's growing role were later lampshaded in a later storyline: when Ataru tried to resign from the post of class president and give it to Mendo, everyone assumed he was resigning from being the main character, with Lum being the exception because she was convinced the main character was herself.
Shinobu was less hot-tempered in early installments and didn't yet have her super-strength. One chapter showing a possible future even hints at her and Ataru getting married and having a child together. As the anime took more cues from the retooled plot and increased focus on Lum and Ataru as a pairing, this chapter was one of the stories that were skipped over.
Mendo was not Ataru's rival in the first volume, but instead his role was taken by four (sometimes five) nameless classmates who would wind up dragged into the strange adventures. Oddly, while Takahashi phased these characters out in favor of Mendo, the anime gave them more roles.
When the Death Note manga first introduced L, he actually stood up straight, but he was then given his slouch when he revealed himself to the Kira Task Force.
L was also depicted with eyebrows after revealing himself, but they quickly disappeared over the course of the manga. Pre-revelation, his hair was more on the curly side of messy and longer, instead of his memorable spiked style.
In a case of Art Evolution, Matsuda looked closer to Raye Penber when first introduced. Mogi's face was also more on the cartoonish side, with his eyes being much wider and bulging.
In the early manga, Light was shown to have two friends from school. The anime adaptation excluded the characters to depict him as more of a loner.
While Mello is memorable for his black outfit and baring his midriff, his initial manga appearance depicted him with white pants and his vest covered his abdomen.
The very first color image to feature Mello and Near (pre-timeskip) had both boys depicted with pure white hair. This was due to Ohba and Obata still struggling with ideas for the two at the time, with one idea for them to be twins (or at least resemble a pair). After their personalities and designs were finalized, Mello's hair became blond in all later color images.
The first couple of chapters of Mysterious Girlfriend X are way more direct about sex than the rest of the series. Among other things, Tsubaki actually dreams about having sex with Urabe. Later in the series, dreaming of mere contact is enough to blow his mind.
The first chapter of the first season of Rosario + Vampire has this effect. Saizo Komiya hulks out into a massive, veiny, humanoid... thing with a snake tounge, and neither he nor Moka gets an entry in the Bite-Sized Monster Encyclopedia that everything else does. In addition, Inner Moka isn't nearly as harsh as the rest of the series, almost flirting with Tsukune. The encyclopedia problem is remedied later on; the bonus chapter to conclude that season provided an Encyclopedia entry for vampires, and it can be assumed that Saizo is a monstrel like the rest of the Anti-Schoolers.
Due to the fact that the movies are made at the same time the new series is being done, it's easy to spot out how different one character acts in one of the Pretty Cure All Stars movies than they do in-series. For example, Erika is easily shown diving into Tsubomi-level doubts and worries in DX 2 where she's shown in the series to be in almost constant Genki Girl energy levels.
Tenchi Muyo!'s first OVA series was much more attached to its harem roots and was easily more sexualized and "mature" (Noboyuki was The Peeping Tom, Katsuhito was shown groping Ryoko's breasts in one early episode, Washu flipping off Kagato, Ryoko and Ayeka's attempts to win Tenchi flat out) and a few characters' personalities were vastly different (Sasami was shown to be a mischievous Bratty Half-Pint, Ayeka was shown to be a little more haughty and antagonistic towards others, Mihoshi was a little more competent than she is now).
This can also be seen in the manga based on the OVA — the OVA rarely had the group leaving the house except for trouble, where the manga had them going all over the place, especially in the later comics where Sasami's seen going to school.
The English dub also took a couple episodes to find it's footing, and originally referred to Ryo-Ohki as a male before correctly switching to female. A couple actors also changed how they voiced their characters (notably Nobuyuki sounds more higher-pitched and nasal in his first episode before Jay Hopper switched to a lower doofus-sounding voice).
Black Butler starts out in some sort of alternate world that's a very close, but not complete, copy of Victorian England. This quickly changes to simply taking place in Victorian England.
In the earlier stories Manga/Golgo13 was much more chattier, even cracking some jokes in comparison to his later characterization as The Stoic.