I personally think there should be a complete overhaul of how Assist Trophies work. The idea of representing more characters is cool, but there's really no gameplay difference between them and Pokemon, which is a bit of a shame. The Pokemon worked well for all 3 games, and can stick around, but some of the Assist characters should feel 'bigger' than just another Pokeball.
I think a cool possible solution would to be to have them as almost like a new special move - you pick your character, then, from a second menu, select an assist trophy to go with it, that could then be activated during battle when certain conditions are met (maybe there can be a super meter or something). Some could produce attacks, some could aid recovery, whatever. This would allow a character like Roy to come back, and be in a bigger role than he could possibly be in now, but without actually taking up a proper character slot.
This would also be an interesting way of implementing that customisation focus that Sakurai seemed to want - you could have four people playing as Mario, but they could all be different thanks to having different assists.