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Pokemon in Smash seems to have loads of references to the anime
There's the Misty and Meowth's Dream trophies in Melee, the anime cries like you mentioned, Mewtwo and Lucario having their anime voices, Event 44 in Melee is a reference to the First Movie, Ash-Greninja is Greninja's Final Smash, Pokemon Trainer's trophy in Smash 3DS references anime characters like Ash and Iris and also the original opening theme, the "Mewtwo - Strikes Back!!" tagline.
I'm sure there's more but thats all I can remember
