Ok, I understand nothing about game development. But here's what I think:
I understand that one of the most dificult things will probably make these characters unique. But in terms of story, do you know how in Spider-Man 2 there are missions you can only play as Miles and other as Peter? So forget about individual characters and think the narrative focusing on teams. For instance, you have a blue and a gold team. And some missions you have to play with the blue, others with the gold, and move the narrative like that. So in the mission you have to face Mystique, you have to play with the team that has Rogue and/or Kurt, and move the narrative around them and develop them as characters there. And so on...
Ok, I know its easier said than done, but I know nothing about game development, so don't mock me.