I think that what would be a good idea towards this is to have faction based quests. The basic idea is that you take quests from evil NPCs and that starts giving you a reputation among that faction, which in turn gives you new quests. Though your choice to follow an evil path makes it so that NPCs from rivaling factions dislike you and won't give you quests. Along with that you will gain a bit of reputation with allied factions and soon you can branch out to support a side that could be either good or evil through your faction selection. It wouldn't change the main story line but I think if the implemented it right it would be even more open and rewarding than just letting you pick good option or bad option in the story line. (that plus you would get quest equipment you want as people playing good guys want hero armor, and people playing bad guys want villain armor)