The Dink Network

Mass Effect actually did the morality thing well. The paragon/renegade scores are separate, so being nice doesn't just overwrite the fact you walked all over people in the past. I remember having both high paragon scores AND high renegade scores at the end of the game(s), for pretty much playing how I felt like. I think that's the best way to play the game, too, because the paragon and renegade scores don't necessarily apply in the same situations; sometimes being a douche is the way to go, and sometimes you can solve situations by being nice. Just having a high score in either stat doesn't always work. (In Mass Effect, that still works probably a bit too often, but the idea is good.)

Also, it wasn't a good/evil scale, but more of a mediator/bully thing. Technically you're still a good guy saving the universe. It worked in the context of that game, but in an RPG where you can randomly murder townspeople and such, a traditional good/evil scale might make more sense.