I actually really enjoy the Metal Gear games so far.
It's disjointed, it's shizophrenic, it's mostly cutscenes, it doesn't make a whole lot of sense, but every game within the series stays loyal to established lore, continuously takes the piss out of itself and keeps you guessing as to what crazy thing Hideo Kojima thought of for the next encounter.
The final conversation with the Patriot AI at the end of MSG2 was actually pretty interesting, kinda doing a Bioshock twist before Bioshock, and not as smoothly executed.
That being said, MSG2 also abandoned what ties to realism MSG1 had round the second act of the game. Vampires, bullet repellant technology etc.