Considering the fact that Game Freak can't figure out the easiest thing to do with Streetpass (battling copies of the trainer or swapping items) I don't doubt at all that they're going to implement amiibo functionality or possibly having problems doing so.
It could be they're trying to print a bunch up, or figuring out if it'd be more cost effective to have figures or cards. Can you fucking imagine 721 pokemon cards?
Personally speaking, I'd like to see special battles against really strong Pokemon using the Smash amiibo. Smash Pikachu, Greninja, Charizard, Lucario and Jigglypuff and then at the end they'll join your team. I'd be a complete shakeup for how we capture Pokemon and also be interesting. Lv 100 motherfuckers that are hard as hell, but ultimately wont be used online (or can't be used online).
Either that, or just give me damn even Pokemon. There's already one of Greninja.