MGS plot is more about ideas and character concepts than a consistent narrative.
Each MGS
movie game makes complete sense in the moment, at least to me. And I've played every game all the way through except Metal Gear 2, and I guess I didn't do every little thing in Ground Zeroes.
I think that has to do with Kojima's style. Each of his games is centered around a particular theme or series of themes. He manipulates the narrative thread to focus on this theme or deliver the message he wants. The reoccurring characters are concepts that have semi fluid roles depending on the narrative:
Otocon/Huey is the brilliant, inept scientist.
Big Boss/Solid Snake/Old Snake is the protagonist surrogate. His condition and dialog is mostly focused on delivering the game's message.
Ocelot as the ultimate double agent, whose goals and alliances are never to be trusted.
Looking at MGS as a concept work and not a solid, interwoven plot has allowed me to enjoy it a lot more. Then again I'm not one for huge, overarching narratives.