Lucario's my favorite character in Brawl, yet, ironically, I dislike him in the main Pokemon series and don't think he's that important...he was chosen for being "now".
Mewtwo's pretty much universal and timeless, and like I mentioned I wanted villains on the roster, and he fulfills it (even if he's not technically a villain, Melee certainly made him evil-sounding and such) better than any other character in the Pokemon series who makes sense to be playable.
I chose Genesect because he's NOW, plus he's fucking cool looking and playing as a giant mecha would be neat. He's got his movie coming out next year, which is when Smash 4 will probably be in the main development stage (Pokemon inclusion does seem to be based partially on the anime, as Lucario was pretty much included due to being the star of the 8th film and advertising Gen IV, and likewise Jigglypuff was probably included based on her big role in the show), and I have a strong feeling that he will factor into Pokemon's Sixth Generation as they'll likely debut his Ancient Forme in the new film, which will probably be an Event Pokemon in the first game of Gen VI.