I would say that a lot of these plot holes can be filled will some logical thinking. Cage was trying to make a realistic story which tends to have subtlety and nuance. Square Enix attempted the same thing with Final Fantasy VIII ten years ago. Modern Warefare 2 on the other hand, has some gaping plot holes and made no fucking sense. People always say that MGS and Kingdom Hearts make no sense but atleast they can make a good story out of themselves. MW2 couldn't.