There is a difference in what the character thinks of himself and what the player knows is going on because of the definitions of the alignments. What the character thinks should have nothing to do with the alignment choice made by the player. You shouldn't give Darth Vader a Good alignment just because he thinks he's in the right; by the rules, he's Evil no matter what he thinks.
That may sound like I'm trying to argue against dropping a D&D sort of alignment system. Actually, I don't really care. I think the D&D alignment system works fine, giving a nice reminder to the players of how they have chosen to play their characters. But I also think that removing it and replacing it with another system, or even nothing at all, won't really change the way characters behave or interact with each other.
To add another thing I'd like to see...
Separate Knowledge Skills. Whatever way characters will be built in the new Layonara, knowledge should come in separate, distinct categories rather than a big lump of a know-it-all Lore skill.
