Levels of game morality
In order to simplify, I'll couch it in term of protagonists, their objectives, and how they meet those objectives.
1. Non-character games. Puzzlers, Geometry Wars, non-personal games in which moral issues are basically non-existent.
2. Good guys doing good things. Same as above, only doing things that aren't questionable. Diner Dash, puzzlers with characters, Professor Layton, etc.
3. Good guys beating bad guys with good things. Again, puzzlers. Also, good vs. evil only with non-violent resolutions, or resolutions not involving death. Old Nintendo Franchises.
4. Good guys beating bad guys with bad things. Action-movie material. Old Nintendo Franchises. World of Warcraft.
5. Neutral/bad guys who have the choice to do good or bad things, but the morality of the choices are obvious. Mass Effect, Bioshock.
6. Neutral/bad guys who have to do bad things or are tempted to do bad things. Morality is not clear cut and must be deduced; the game will not make the morality clear for you. Army of Two, tangents in certain RPGs, Grand Theft Auto Series.
6. Bad people who do obviously bad things. The game only progresses if you do something obviously morally wrong. Super Columbine Massacre RPG is the only meaningful one I can think of.
The problem is that people put GTA in category 6, not 5. The problem is also that none of these are inherently bad, but that we often need to hear from players and reviewers before we know about these systems. Also, those ignorant of video games are unaware of these systems and thus must agonize over the games when it's obvious that they shouldn't have to.
If we must make solid, governing ratings, we should do more from the morality systems inherent in the game world and the potential and inevitable actions of the characters, not simply by what material exists.