I think the overlaying storylines aren't that bad actually. MGS was a sort of Greek tragedy, MGS2 was... well ignore that one. MGS3 was a story of betrayal and patriotism and MGS4 was among other things the story of an old man who is nearing death and his life catching up with him. And as said even a lot of the blatant wtf moments (which there were a lot of) like "I live on through this arm!" are presented in a way that doesn't make you turn off the consol in exasperation. And the games do touch on some really interesting subjects like cloning, that whole situation with Naomi, her parents and Grey Fox, loyalty to your country, world issues like nuclear weapons, the increase of PMCs ect, ect. . I'm not saying it's one of the great works of our time but there is some substance there.