First they need to vastly improve on the style because, while some seem to like it, the reaction towards it is largely negative because we've seen better models on the N64. Then the combat needs to be made WAY deeper than just button mashing until everything dies. I don't know, maybe they could incorporate a fighting style with some influence from the batman arkham games and have more attacks, combos, a block button and gamepad features. Every included pokemon would need to have much more definable strengths and weaknesses too, maybe for example blastoise can soak up more hits than charizard and he charges his cannons so he can use them to take out a large number of oppenents at once, whereas charizard can dodge more and attack more quickly and aggressively. Having said that this would be difficult to implement for a game with 649 playable characters but I suppose they could make it easier by splitting the pokemon into different categories. AND IF THIS USES THE TOYS AS AN EXCUSE TO DO A SKYLANDERS I'LL BE SO SAD.
Anyway I'd love to see them do a 2D or Tekken style pokemon fighter, with maybe 30+ pokemon with the non playabless being assists and arena hazards. I'd urge them to stray away from just having humanoid fighting types though, a diverse roster is a great roster, and pokemon has the characters to offer that.