I actually like the Supers to K.O. system, because I don't need every game in every genre to be a complete 1:1 clone of another game. I thought it was fun, especially getting together with friends to play co-op.
With that said, I think a followup should have more options in how you play. Have a "Classic" set-up, with the Super system as is, with some refinements, and then have a different system/mode, where you can do it health bars instead, with Supers being used to take larger amounts of HP from characters instead of an instant KO. One of the things that disappointed me the most about All Stars was the lack of real modes/options/extras in the game. I wished there was more of a character museum, concept art, jukebox. Presentation was sorely lacking in this game, but I still play it regularly, on the Vita on bus rides to and from work. I think it's fun, and a sequel could really add so much that was missing here.
I'm not so much concerned about character roster, as I felt the current roster is pretty good (but then again, I'm a huge PlayStation 1st and 2nd party character fan, so this game had more than a few of my favorites already), but I'm hoping we'll get a surprise, maybe digital only sequel on PS4 if they aren't confident in it pushing units at retail. I'd definitely snag a PS4 version of the original. Now, with the library being as small as it is, would be a perfect time to grab some new people who are really looking for something to play on their PS4s. People do seem to like the game when they play it and get past it not being a Smash clone (I love Smash, by the way, and am going apeshit waiting for the 3DS version to finally drop. I just want it so bad, dammit!).