In GZ you never see the Surgeons face, this was intentional as he is “Venom” snake, Kojima gave him that name cause this snake is spreading hate and crap everywhere with people like Eli and all that, and is screwing up the Boss’s rep. At the end of the game I am betting it will come around to MGS1 showing Solid kill this guy instead of the Real BBoss, which would be lamesauce. Back to Ishmael, that was Boss, he was way to hardcore and he just dissapeared when Ocelot ( who loves snake) appeared, also notice how Ocelot doesnt take any crap from Venom….Cause he isn’t the boss!
Also, Chico and Paz, paz is supposed to be dead. We know this, but Chico is gone? So….Maybe with all the surgery Chico now looks like Paz..Ugh..That would be creepy, but would explain why she looks a bit different and gets all screwy when confronted ( as has been done in other things with hypnotized characters) So, maybe like in MGS4 with Ocelot they hypnotized Chico into thinking he is Paz just to help the whole Venom snake thing.
As for Mantis…maybe he is moving salubot around, which is the only explanation why it is able to be so advanced.
Last one, Master Miller. Dudes eyes are all funky, much like the parasite things. So perhaps he is now a possible carrier of it? Maybe the thing that eventually becomes foxdie or something since he had contact with Solid and Liquid?
If youve beat the game, feel free to laugh at how absurd some of these are, if you havent…well join in!?