Personally, I'd love it if the newer generations weren't represented. Each addition only further suggests that Nintendo doesn't care about the quality of the franchise anymore...as long as there's another Mewtwo or Pikachu clone, it doesn't matter that the other hundred or so were literally crapped out in a drunken brainstorm the night before. Fans will still rave because X is so cute/badass.
That said, much as I have come to loathe the Pokemon franchise, even I wouldn't be so selfish as to omit a Victini or Zoroark cameo. Sakurai may have his idiosyncracies, throwing in bad ideas like Landmasters and waterguns and TRIPPING, but he's not stupid. Victini alone would probably account for a massive increase in SSB4 sales. The selections thus far have always been heavily influenced by the anime, and I don't see any reason why that should change, given that without that medium every pokemon would have the personality of a rock.
BUT, in a perfect world where only first gen mattered, my Pokemon reps would be as follows:
Pikachu
Jigglypuff
Mewtwo
Pokemon Trainer
Maybe, MAYBE Meowth
Also, first post. Been browsing this topic for a while and wanted in. Most of you seem of the rational, friendly type.