Smash Bros. does have some Pokémon characters that you can use, like Charizard and Greninja. But, there aren't enough playable characters for a Pokémon-centric fighting game. Enter mods.
Thing is, Smash Bros. games do include the character models for plenty of Pokémon, for use whenever you throw Pokeballs in matches. Sleepy Jirachi seems to have gone ahead and made use of these character models for a Brawl mod named "Pokebrawl," and while it's only in beta right now, it already looks great. I say that as a huge Smash Bros. fan, though — this appeals to me more than a Pokémon fighting game in the style of Tekken. I'm also a fan of the character selection here: you've got obvious Pokémon, like Blaziken. But there's also interesting additions like Rotom, Jirachi and Darkrai:
Right now, the creator is looking for collaborators to help with the modding — here's hoping that some people sign on, because the project looks really cool.