I assume you're talking about the true story mode. In which case what I'm hoping to see, mechanically, are stories that are divided into chapters, but you play them in more-or-less chronological order (although some chapters would likely have some overlap in time). The stories would be based on subplots rather than by characters, so each story would involve several playable characters, who join or leave the party based on what's happening in the story at the time. It would be cool if for each fight, you could select your team based on the characters in your party, although for some fights certain team members may be locked in/out if the story requires it.
Overall I think you can just play the chapters one-by-one which unlock the next chapter, until you get to the ending chapter. Maybe at some points, certain parallel chapters could be unlocked at the same time that allow you to play in any order, but all of them will need to be completed in order to unlock the ending chapter.
Maybe there could be optional "side story" chapters that are based on less-serious/important subplots, which could involve the less-plot important characters like Beowulf, Robo-Fortune, etc.
Personally I don't believe in doing "RPG" mechanics like levelling up or unlocking certain characters or moves based on which chapters or routes you have played. I think they should just concentrate on telling a good, coherent story, and not having to worry about balancing unnecessarily complicated mechanics. Same thing goes with doing multiple routes or endings - I'd rather it be a good linear story.