Different paths. It can be done with several main arcs, but highly nonlinear games are in somewhat short supply. I would much prefer the ability to choose my overall path, preferably with several "good", "neutral", and "evil" paths that you can take your character.

Generally though you will define the main character's personality through your choices. A Baldur's Gate-like system'd probably work best in this, where you get to choose from several different dialogue options, some wildly different.