Yeah, that'd be a nice change. It would even make more sense if they made the two versions completely different from each other (although Black and White already has such feature).
tbqh, I thought GameFreak would've already done something like this right after I've played Gen II. I'm speaking about rivals. I mean, even if it was just on the Rival's side, it would've been so interesting to have 2 stories to follow in a single game. Aside from being just a boy-girl selection, you also get to know their sides of the story. Their adventure. The reason why they keep stalking you and such.
I'm glad Gen V made the change because things were just getting old.