I read somewhere that the Cobras were representations of the emotions Kojima had to go through while making MGS-3, i guess that could explain why they feel out of place in some ways.
They also line up pretty well with the Five Stages of Grief
Oh, and MGS4 was a good look at the dangers of the military-industrial complex and the psychological effects of war. Yeah, way too much stuff was handwaved with nanomachines, but that wasn't the point. The plot is just a vehicle for the larger themes, and really it's kind of a wonder they manage to make the games' plots line up as well as they do at all.