I always liked the idea that faces were legitimate badasses, not smiley little pretty boys (Kingston and Morrison). Look at Randy Orton, that's a pretty good example of the way a face ought to act these days... maybe not acting like a convulsing snake, I hate it when he drops to his fists and pounds the ground, he looks like an idiot doing that. But his overall gimmick is pretty damned good. They should also be getting clean wins.
Heels on the other hand should (IMO) only win cleanly if they're actively being pushed to a new bracket (development->openers->midcard->main eventers) otherwise they should lie cheat and steal their way to victory. It's the classic method and I've always preferred it that way, otherwise they take all the popularity from the faces, and make it VERY hard for a face to get over unless they become a tweener.
These days top faces are usually heels that get over in spite (not because of) their gimmick, like Austin and CM Punk, or have been consistently good for years and years and years, like Angle or HBK or HHH.
Being a rookie face is an almost impossible job now. Anyone remember The Lightning Kid? Yeah, maybe you'll remember who that is if I told you he got a new name after he pulled a upset on Razor Ramone? Remember the 1-2-3 Kid? Still kind of a tool but at least you should know who that is. But remember Sixx-Pac and X-Pac? ... Kinda reminds me of Evan Bourne.
Seriously, who was the last rookie face to get over with the fans? Is there ANYONE that debuted as a face and stayed face to get over with the fans since Bill Goldberg? I suppose you could sort of argue Daniel Bryan.
In the end, I think it's not the faces that need to be booked differently so much as heels that need to be booked differently.