Just one thing -- the idea of the aliens' involvement in human history predates Däniken by at least a century, and his work is overall of such a dodgy quality that someone as knowledgeable about lore and myth as Lucas would probably not base this storyline on Chariots of the Gods.
While that makes perfect sense (and I know about the theory of aliens being involved in human history being around forever) "Chariots of The Gods" was cited to me as somewhat of an influence on Lucas' INDY IV plot idea by someone within Lucasfilm as far back as 1999. And Däniken was indeed among the first to attempt to tie the Crystal Skulls themselves into the whole lore. It's worth mentioning... especially when people still seem surprised at the idea of alien stuff being mentioned in the movie at all.