like the ability to walk on water and survive gun shots to the head and possess people through surgical arm implants?
The series takes place in another reality where things like photosynthesis can keep an old man alive. Vamp, as I said, was a vampire. Originally, he was supposed to be this martial arts guy. Maybe they wanted his running across water to be like ninjetsu? lol
As for possess people through surgical arm implants.
Liquid is by that time a ghost, and would have the unfinished business of Outer Heaven. Ocelot on the other hand was the offspring of The Joy and The Sorrow, right? Ocelot has the special power from his father (was a spirit medium) to play host to a ghost. Binding Liquid Snake's arm to his body would bring with it the undeparted ghost of a man fixated on living on achieving his father's goal.
There's a lot of crazy shit in MGS, but it's usually just presented as crazy. There's a sort-of logic behind everything.
MGS2 was loopy and off kilter, but as other's have stated, it was part of the simulation.
Lastly, someone said something about Raiden being totally gay. That's just a too-bad mistake. Kojima was actually trying to make him a seriously cool character.