Hell, I don't even know who the actual villain is in MGS4.
Personally, I find that to be an integral part of the experience. In real life there is never a black and white 'bad guy.' Why should videogames be any different?
Maybe I didn't explain it too well, but it's not that I don't understand the morality of the characters, it's that I literally do not know what any of the characters are trying to achieve. There's two different AIs that I can never keep straight but they were both made by the Patriots, and there's Ocelot who wants to fulfill his mancrush on Big Boss' dreams, and UN-sponsored forces who want to stop him (for the Patriots?), and I don't know who Campbell is supposed to be representing at this point, and Raiden's fucking crazy, and the entire moral underpinning of wanting to stop Ocelot or defeat the Patriots is kinda lost when you don't know who's actually on which side of the question, let alone the allegiance.
That was one of the things that struck me about Snake, in that he completes his evolution into the Perfect Player Character - his in-story personality is that he does whatever the last person he talks to tells him to do, with a grumble and some smoking, while he searches for a good way to kill himself and end the story. He just
does not care anymore.