I don't really have any ideas that weren't brought up here before, but I'm gonna list my top five wishes anyway.
An option to create custom maps. I don't necessarily mean anything to the extent of SG base building, I'd be entirely content with a selection of premade rooms and corridors to fit together.
More control over placement of details like bosses, destructible objects or even Giant Monsters.
More power sets to choose from for custom enemies, hopefully including pool powers or just an optional tertiary powerset.
The ability to customize enemies' power effects in the same way as for player characters.
More clothing options for custom NPCs, especially from enemy-exclusive costumes.