I believe there were some past topics about a Solid Snake (aka David) character build, but I thought I'd reopen it. More or less, I think it would just be along the lines of an infiltration rogue with a high Dex/Int and above average Str/Con. He would also be an equipment junkie, carrying an item for most situations. Facing the reality of pathfinder scores, Charisma would likely be at the bottom of the list.
Assuming Human of course, I think it would be good to swap the bonus feat for focused study (starting with stealth), eventually get a repeating crossbow or put a single level in gunslinger. I considered full gunslinger, but it's almost like you're Revolver Ocelot at that point. You'd also have to possibly get Improved Unarmed Strike to compensate for his hand-to-hand skill.
As for Ocelot, full gunslinger with quick draw, rapid reload, pretty straight forward.
Big Boss would more or less be the same as Snake except maybe different alignment and more priority on charisma/leadership (despite them being clones, I was just thinking about the charisma when you consider the different paths of their lives). Assuming the much older Big Boss. The other characters I'd be interested on hearing opinions for are Raiden and possibly Liquid or Solidus.
Solid Snake scores (rolled up using 4d6, drop lowest)
Str 15
Dex 18 (Human +2)
Con 13
Int 16
Wis 12
Cha 12