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