Being able to customize movesets has always been something I've wanted in SSB, since before Brawl was released. I'd love if that was the customization he was referring too. Imagine playing Mario on your 3DS version, going through the story mode or whatever, and unlocking cool moves. Then you can customize him and pop him onto your WiiU to play with friends. Maybe you unlocked a new B-up so he uses the F.L.U.D.D. jetpack instead of the punch. And you swapped out his bouncing fireballs for an attack that shoots starbits. But then your friend uploads his Kirby, who swapped Final Cutter for Hi-Jump Kirby and instead of having Hammer Kirby on Side-B, he has Fireball Kirby. It would lead to many, many, many more balance problems, but it would open up the door to so much.
The other thing I've always dreamed of was Alternate Forms for characters. You would have the normal "Four costumes per character" with the same attack, but you could also switch to a different form of your character after unlocking them, one that plays completely differently. So when you start a match, you move your chip to Mario. But to mix things up, you change your Mario Form. You skip over Dr. Mario and go straight for Paper Mario, who has a whole different moveset and is much floatier. Kirby could have Yarn Kirby. Zero Suit Samus would become a new Samus form. This would allow the introduction of characters that were really similar, or in effect the same, without having to clog up the main roster list with too many people that would be knocked as "clones." Another option could be to reuse Fox, Falco, and Wolf down to one character, just Fox, but with Fox and Wolf (and hell, why not more?) forms you can switch between. I don't think this will actually happen, though. I should be clear about that. It would be a massive increase in the number of characters if everyone was just given one extra form. I just think it would be my ideal way to balance the desire for more characters against the limits of double-dipping in a character or cloning, which always bugs people.