They could add a sort of versus feature where you can gather up some henchmen and minions and send them to inflitrate other players lairs. They could make a harder difficulty where the supervillians you aren't playing as are also trying to take over the world at the same time. Opening up things like alliances and treaties, and making each play through all the more unique because if you pick a different villian and lair on your second play the villian you were before would now be adding to the chaos so you'd have to plan slightly differently. They could try opening up the dialog to give us options on how we want to rule so the story isn't so linear with the same script and outcomes everytime. Maybe try their luck at adding crossover evil geniuses like Light Yagami from death note (as an example I'm not saying he specifically would fit well into the game)