Note that the best examples of the non-linear make your own character's alignment games are American games. That's because for whatever reason Japanese game makers don't seem to want to do that.

The Japanese "silent hero" stereotype would probably bother me a lot less if you could actually make the hero's decisions what you would do. I've resigned myself to the fact that JRPGs are there to tell a story, so it annoys me when what seems to me like they try to have it both ways. It's kind of like you want to shout at the game "if the hero is supposed to represent me let me make my own damn choices!"