As has been mentioned elsewhere in this fine thread, I believe Nate, Chloe and Elena looking for the truth behind the legends and myths surrounding Atlantis would be an excellent adventure. Please, Naughty Dog, consider it.
On an offbeat note, how about Nate, et al., getting involved in an adventure linked to the long-lost, mythological Amazon Nation? (The Amazons were allegedly a female-dominated nation that once existed in the Black Sea area and North Africa, around Libya.)
How about Atlantis? Not saying that's the only location Drake goes to, but it would definitely be cool to see ND's imagining of the Lost City.
EDIT: Dammit, the guy right above me already said it. I'm sure it was said earlier in the thread, too.
Everquest Online adventures
God of war Series
+ Dark Souls.
Personally I think Uncharted 3: Lost City of Atlantis would be awesome. One individual mentioned wanting more scenes dealing with underwater game-play, the other mentioned Atlantis. Obviously much of it would be "Land based" A battle on the open sea between two naval ships would be fun as well. Perhaps, the two vessals fighting (the one nates on hull is breached; he is forced to jump aboard the enemy vessel?)
Just another idea...