Since when did knowing CQC > Every other unarmed fighting capabilities in the world?
Oh, and I believe Snake is at his prime in MGS 1 (the Twin Snake's is his strongest performance yet by far). Kojima stated he was as a man in his 50's in MGS2 while he was only 38 years old.
Liquid/Ocelot comments on that as well. "Drowning in time I see, I know what it's like brother" and "the price of physical prodigy, a few more years and you'll be another dead clone of the old man".
I don't think he was quite on par physically with his MGS1 self, and the experience and techniques doesn't seem to be that much different. In MGS1 he pretty much knew what he needed to know.
Btw, Naked Snake's venture into the jungle was his first jungle mission as well. He says he's trained in urban areas, but that doesn't slow him down one bit even in his first mission. Unless this is a later incarnation of Naked Snake like Portable Ops (shouldn't he be called Big Boss in that case?) I don't see him having a MAJOR advantage, especially since neither are given camoflauge. After all, what Naked Snake would've learn't most from those missions is camoflauging and hunting, where only the latter will play a part in the scenario in this case.
And tracking would count as well. SS says that BB was a master of it, but that sure as hell wasn't in Snake Eater. He never utalizes it nor shows any knowledge of it. (Especially since his prior missions were urban one's). So I'd say it's safe to say it that was something he learn't later (like Raiden did, after travelling the world).
I could be wrong though. :/