^No, not at all. In fact, I think its a great idea. This way, we would have two storylines instead of one. Yet, they wouldnt have to have an enemy for every character because there wouldnt be a storyline for every character. Tremendous idea.
Here's a question: Win you choose either good or bad (use good as an example) do you think you would remain one (good) character the entire time, or would you have to use EVERY single good character in individual matches?