A question...

Have you ever written a fanfiction where you only take a few things from the fanbase (e.g. a single Pokémon) and then use your own imagination for the rest? Would this be considered as fanfiction? I'm currently plagued with this as I'm in the planning of a fanfiction that only uses two Pokémon for the whole story (so far).

I would say yes, since you're using Pokemon as characters. I don't know what you mean by using your own imagination for the rest, but since you're writing about Pokemon, it can count as a Pokemon fic.

I think I know what you might mean. For a RP of mine, I use lots of inspiration from Homestuck, but I also tweak enough of the mechanics and story and features so it can't really be called a Homestuck RP anymore. I take the game they are playing in canon (SBURB) and change it and give it a new name, for instance.

As for pokémon... I'm not sure - if it's about pokémon, as Astinus says, it's about pokémon. That counts as a pokémon fic. I guess the line between what is fanfiction and original fiction can be a bit blurry. But in pokémon, it's fairly clear that if you incorporate a pokémon of some kind in the story, it's a pokémon fic :p

I have not personally written any stories like that, no, but I have seen very many that have gone the same way. I really don't think anyone cares if an imaginary Pokémon quota is filled or not, so long as it's a good story.