Just imagine this, Super Smash Bros 4! Now with evn more characters but the only ones in the game are Mario, Link, Kirby, and Pikachu! So now you have to go out and buy more characters, Yeah! (my wallet is crying right now).
Skylanders works just because it's a full single player game so having 3 characters at the start doesn't hurt, fighting games on the other hand would have a difficult time trying to get additional NFC characters to work.