Make some of the available AT power sets available to other ATs. For one thing, I would love to see an Assault Rifle/Super Reflexes or a Fire/Invulnerability hero, expanding the no. of power combinations.
Along those lines, I would like to be able to make a hero that was Empathy/Kinetics.
How about a non-agressive NPC ambush? You are going about your business and a bunch of bystanders see you and come after your autograph. Then, one of the bystanders attacks you and you have to figure out which one.
More toon customization options, including animal and alien features. Perhaps a standalone toon creation tool that works offline and creates a file that can be opened during the toon creation process in game.
Vehicles.
More mission locations. How about indoor missions that take place in a ship? Or missions inside pyramids or other exotic locations?