Sailor Moon: The original English dubs of the anime. Are they worth watching or are they dated, horrible Macekres only worth watching for nostalgia (and even that is arguable)? Most fans have a negative view on the dub and mock it however others honestly enjoy it and think it's a good dub (especially for its time period). Then there are those who enjoy them for how hilarious the dubbing, censorship, and voices can be instead of the quality of the dubbed version itself.
Misty's departure pretty much split the anime fandom into those that won't have anything to do with any episodes past Johto and those that openly embrace the newer episodes.
There's also a divide between people who like the anime and people who think it does more harm than good for the games. The latter tend to want an adaptation that's truer to the games, like Pokémon Origins.
Yu-Gi-Oh!: With the fifth series, Yu-Gi-Oh! ARC-V, there was a split between its fans and the fans of Zexal; while the fandom as whole has always discussed which series is "better" to various levels of seriousness, you'll seldom find any consensus reached in between these two fanbases, let alone people who like both series. The reasons vary according to who you ask, but mostly it seems like Arc V fans think of Zexal as the Dork Age of the franchise, while the Zexal fans look down on Arc V for considering it too ambitious or convoluted for their tastes.
Fairy Tail fandom is extremely divided on the subject of Jellal Fernandez. A major player in Erza's backstory, he made his appearance in the Tower of Paradise arc, which concluded with the manga's hundredth chapter, although technically, he'd been around since the second page of the first chapter. He has appeared in every single arc since then, in some form or another, and opinions are very mixed on if this is a good thing or not. One large segment of the fandom thinks that the unfolding drama is interesting, another thinks that he's worn out his welcome and needs to go away for good.
Naruto: Uchiha Itachi's true backstory. At least in the American fanbase, this plot twist split the franchise right down the middle to absolutely polarizing extremes. Those who loved the plot twist venerate Itachi as some kind of tragic hero, while those who hate the plot twist continuously paint him in a bad light or make him as Wangst-y and obsessive as possible. The split created some of the strongest sections of the Naruto Hatedom, some of which last to this day.
Slayers: The third anime season, Slayers TRY: in the late 90's/2000's when it came out, it deviated in formula and story from the first two seasons (darker plot, downplayed humor, and one villain to chase as opposed to a multitude), and the main characters become peripheral to Guest-Star Party Member Filia and antagonist Valgaav. Because of this, it's either the most well-loved season or regarded as a piece of crap - it's even referred to as such by some professional reviewers.
Science Ninja Team Gatchaman: Science Ninja Team Gatchaman vs. its multiple English adaptations. While Battle of the Planets is lambasted for turning the franchise into a joke and being one of the early examples of Macekre, there are just as many fans that will defend the flaws present (or love it in spite of such) and insist that it is the superior dubbed adaptation by the fact it came first, had a high budget, and was a source of much '70s childhood nostalgia.