Not wading through all the other suggestions, but I'm sure everyone proposed 'new content' of some sort. Here's my two cents.
1. Revitalize Perez Park and Boom Town. Give us a reason to go there. Zone centric story arcs there would be great.
2. New Zones. Underwater Zones similar to Atlantis. Winter Zones.. other than just the holiday zone.
3. Power Sets. Hard Light Constructs power sets. Stretching Power Sets (Mr. Fantastic, Plastic Man etc..) Shape-Shifting Power Sets.
4. New Body Types. Teens, Children (you'd have to limit costume choices.. otherwise it could be creepy), Obese (maybe a slider for that?)
5. More movement options. Web-swinging (Grappling hook/Acrobatics?). Vehicles.. with customization options. Motorcycles, Cars, etc.
6. Complete alignment system. Every mission choice gives you an alignment point. Do the bad thing, get a villain point. Do the good thing.. you get it.