I'd like to see 3 or 4 shorter storylines ala the GTA4 DLC. Have them intertwine or come together in a more meaningful way than in GTA4 though. I like the way missions have worked in recent GTA games.
I'm playing Suikoden 3 right now and was thinking about something similar. S3 uses a Trinity system, kinda like 3 sides to a story.
You play 3 or 4 chapters with completely different characters, let's say a lawyer, a criminal, and a cop and after a time the complete story unfolds and you can choose with which character you want to finish the game and see a different ending each time.
I especially like the fact that the NPC act different when interacting with you based on which guy you play.