The way that save files are generated and displayed will be a nightmare on multiple play throughs. Removing a group of saves I don't care about after a certain point rather than having to guess and overwrite it, as well as being able to see a fresh games saves seperate from other games would make it far easier to replay the game multiple times without it being an issue keeping other play throughs available to pickup and continue when the fancy strikes.

Umm, just name your character something different. Then the saves get seperated by character name. Yes, you do have to play through the intro again, but is it that bad?