I would love to see an adventure set either in, or including:
The Caribbean - Jamaica specifically
Central Africa/"The Dark Continent
New York, circa 1960-1964
A snowbound location along the lines of Nepal
Start the pre-title adventure off in Jamaica - and then go from there. We go back to the States and end up in 1964 NYC around the World's Fair. Perhaps Jones is meeting some mysterious agent there who has contacts him with clues about the MacGuffin, and in the rush of the crowd, this contact is killed and Jones gives chase of his murderer. Jones then follows the clues to this latest MacGuffin or follows his enemies to different locations. A nice sequence in each.
This would be an adventure not instigated by some outside body, but by Indy's own desire for some object which has eluded him his whole life. His version of the Holy Grail - the obsession that his father's entire career. We've spoken before about the nature of obsession in Indiana Jones - how each villain, and also Henry Sr., suffer from it. We've never seen what Indy's obsession is. The ultimate piece of fortune and glory.
Forget South America. Too generic. If we have to do the Middle East, let's do a part that we've never explored before - the Promised Land.