Just finished the game, my fresh thoughts...
1. I felt unsatisfied at how surreal the story was. What I chalked up to hallucinations due to the bone fragmented in Phantom Snake's head ended up all being explained as real.
I dunno, if anything this game seemed less surreal than previous MGS games to me. I think weird shit is part of MGS' identity. Without it, it'd just be a Tom Clancy ripoff.
2. Was the gas-mask wearing child real? How could they fly? Parasites?
That was Psycho Mantis from MGS1. I don't know if they ever explain how he can fly, for some reason Kojima likes to give a bullshit sciencey answer to everything except for telekinesis. It seems that's just something that exists in the MGS world.
3. How are the Snakes' voices exactly the same?
Medic already had a similar voice, people figured out that Medic's voice in GZ was also provided by Kiefer, just manipulated to be much deeper. Presumably they manipulated his voice during the plastic surgery. (Not sure if that's even possible, but it doesn't bother me in a game filled with gundams, angry fire zombies, and psychic kids.)
4. We were in Africa and didn't get to see kid Raiden at all? I thought Eli was Raiden at first. Missed opportunity much?
Eli was Liquid. Raiden would've been 1 in 1984.
5. Paz just... somehow survives GZ and comes back to sit on a bed the whole time? Something else I thought was a hallucination but seemed oddly real.
Keep playing that storyline.
6. Same with Volgin. How is this scientifically possible? I'd say it's a hallucination, but tape recordings referred to him as real, unless Ocelot and co. knew about the hallucinations and simply played along with them.
Supposedly Volgin didn't actually die in MGS3 and was kept alive by his desire to get revenge on Snake. His fire powers came from Psycho Mantis, I believe.
7. Can someone explain exactly what real Big Boss' motives were in the end? Is he working with Zero? What's their ultimate goal? Why does Phantom Big Boss go on to be a villain in MG1 and real Big Boss in MG2?
Big Boss had just lost everything he had built due to being too trusting of his allies. He goes along with a plan hatched by Zero and Ocelott to use Venom as a decoy so that he could go into hiding to work on his real plan of bringing to life Outer Heaven and Zanzibarland. It seems likely that at somepoint Diamond Dogs was folded into Outer Heaven and Venom took over the day-to-day operations of that as he began Zaniabarland. That's conjecture on my part though.
Zero was acting against the interests of the rest of Cypher by wanting to keep Big Boss around, he still saw him as a friend and comrade and wanted to see him return to Cypher at some point.
Ocelott's true allegiance was to the one true Big Boss. After the Prologue though, he's hypnotized himself into believing that you are the actual Big Boss so that he won't be able to blow his cover.
Other than that, another great postmodern game from Kojima that truly bent the mind. A lot of my questions can be answered with the line "There is no truth, only interpretation" from the game, I'm sure.