In terms of what I thought was sh*tty, I'd have to say that
Spoiler:
having those retarded looking arm things as the only enemies throughout all of Shadow Moses was a bad decision. Imagine how it would feel to play through that section of the game while facing actual guards again? It would have been terrific. Also, nanomachines pretty much became the MGS version of fairy dust. They're used to explain everything that seemed like it couldn't possibly have a normal (as far as Metal Gear goes) answer.
Spoiler:
The nanomachines being the answer to everything was pretty much bunk. It cheapened some of the few mystical connections Metal Gear had, such as Vamp's immortality. I mean, in a series where there are real psychics and ghosts, why is it any stretch of the imagination to have a real vampire?