I don’t give a F about the anime origin or the “too many Gen 1” complaint. All I want is Meowth even if it means having to break the anime origin rule with Jessie and James and face the “too many Gen 1” backlash.
I think it's silly to focus on what generation a Pokemon comes from, given that some stay relevant and renewed for ...well forever.
Jigglypuff is surely just a gen 1 pokemon, but the original starters are in almost every generation as a means of a gift, often even in the story (gen 1, 2, 3, 4, and 6 all give them to you in story).
But I also think that a Team Rocket without a Wobbuffet would be ridiculous.
Aside from what Arcadenik said, Ash in the Melee intro and Ash-Greninja in Ultimate isn't anime enough?
I just rewatched the Melee intro three times... there isn't a human character from Pokemon at all. Please explain to me where specifically you think you saw Ash in Melee.
For that matter, please show me where Ash Greninja is in Smash. Is it a spirit? It is definitely *not* a costume for Greninja.
That said- some definite anime references:
Goldeen being useless in a Pokeball, instead of Magikarp, is a reference to the anime.
Pikachu's down B is a reference to Pikachu capturing the thunder from a cloud in the anime in the second or so episode (as thunder was never from a cloud before that point).