I think it's partially a leftover component from childhood. Every generation brings a new thing for people to argue about.
Gen 1: The "which starter is better" was the main point of debate.
Gen 2: This brought the beginning of genwars, and whether adding new Pokemon is a good thing.
Gen 3: The biggest debate that came out of here was people not liking that you couldn't transfer your pokemon, and people didn't like how much the mechanics had changed (at first).
Gen 4: Too many evolutions, too many legendaries.
Gen 5: Too many new Pokemon, whether gamefreak is running out of ideas.
Gen 6: New type? Forms? 3D? We'll see.
People joke about how the Pokemon franchise never changes, but in reality, it changes a lot. The roots always stay the same, but every generation is really different from one another. It isn't like other series where you can see a progression over the years, because each generation is made to be released on another console. So each jump to the next generation is always really big. Change is a natural catalyst in disagreements, so people begin to separate based off of what changes they want, and don't want. Also, the more generations that people can compare to one another, the more likely they are to search for the "best" and the "worst" in everything.
It's also different from the Animal Crossing fandom simply because it's much bigger. As anyone who has played Call of Duty online before, knows that the more people that are playing, the more likely you are going to have people who are mean. Bell Tree doesn't see it a whole lot because the forum is decent sized and the trolls and bullies can get weeded out pretty quickly. A bigger forum simply can't monitor as many people, so you are more likely to have problems and bickering because there aren't enough mods to contain everyone. So the same goes for the Pokemon fandom. It's so big that not every argument can be broken up. The only choice of the rest of the fandom is to simply adapt to the environment by becoming more vocal, or they can simply leave.
I looked into this more than I probably should have.
Aww. Everyone made up while I was still being negative. For the record, I still love you all

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And I think the cutest Pokemon are:

and baby Stantler from the anime.