So, I was thinking there are a couple of things that this game could probably do with. Let me know if you agree!
1. When Pokeballs and Assist Trophies are implemented into the game, there should be an extra option in the Item Switch that lets you toggle if certain Pokemon/characters will appear for not. For example, I like Assist Trophies in Brawl, but I really hated the Nintendog and wished I could toggle it off. It wouldn't have to be a Low/Medium/High thing, just an on/off toggle for each appearance.
2. A 'Stage Hazards' option you can toggle on and off, that'll make it so all you have to worry about in each stage is the layout. Playstation All-Stars is doing something like this, and I thought it would be a really good idea for more competitive play.
If any of these are already being worked on, never mind.