Well, as far as how Pokémon look in my head, they pretty much look exactly the same as they do in the anime. However, the main reason why that's true for me is because everything in my head that has to do with Pokémon fanfic looks like the anime, including how humans look, how buildings and flora look, and what the general aesthetic of the world looks like. That remains true even for stories that don't actually take place in the anime universe at all, which means that for a story set in, say, the game universe, what would normally be either 2D sprites or 3D cel-shaded graphics essentially become "anime-ified" (for lack of a better term). That said, what I'm somewhat unsure about right now is whether or not this "animefication" should be considered simply an abstraction of fiction - or in other words: not actually reflective of what Pokémon and the world around them look like in-universe, but is nonetheless how they're projected in the real world for the sake of art style and/or sanity in the writing process - or if they actually do look that way in-universe, and that none of the characters question anything - or are even aware of anything "wrong" - because that's simply how reality is in their world.

Meanwhile, things are a little bit different when it's time to actually write stuff down. Because I typically try to write under the assumption that the reader has no idea about Pokémon or what they look like, that means that I'll also try to do a bit more than just provide a stylized, cartoony description of a Pokémon matching the stylized, cartoony aesthetic of the anime. I'll also assume that such "non-fan" readers will be using real life as their primary reference for what things look like, rather than an anime that they've never watched. One strategy I've thought about is to use the closest equivalent real-life animal as at least a partial reference for a more "realistic" level of description. So if I wanted to describe, say, Typhlosion, who is essentially a giant fire badger, I would base him first on... well, a giant badger, and then add in the more fantastical elements from there (although I'd also probably literally refer to him as a "fire badger" at times, if I'm feeling particularly lazy). However, such a strategy probably wouldn't work so well for something like, say, Pikachu, who despite being called an "electric mouse", doesn't really resemble a real-life mouse at all other than the absolute basic shape and concept of one. In cases like that, my description would probably lean more towards the simpler side of things, reflecting the simpler and more cartoony nature of the Pokémon being described.