[An interesting side note is that in the IJ films, Indy actually doesn't always beat the enemy to the artifact (or he doesn't hang onto it for long even when he does) -- the enemy is beaten not by Indy outpacing them, but ultimately by their own arrogance.]
Anyway, I have at least one idea for the temple that I rather like. A previous post talked about ambiguous characters, and one of the great dramatic highlights of the films is when there's a big Double-Cross. It seems like the game could potentially capture this in a simple way: when the enemy "catches up to you" in the temple (whatever that means), any ambiguous characters that you've taken as an ally are revealed as either loyal allies, or traitors. And then...something happens to you (?)...you lose the artifact if you're carrying it, or some cards, or something like that.
But wait, who said anything about theme cards being taken as allies? Well, one thought that emerged in the last version was that theme cards, instead of staying put, could be picked up by the players and carried around, as allies. The intended effect was mostly related to the information hunt -- to get higher level clues, you had to have multiple cards with the same symbol all in the same place at the same time. But maybe if theme cards provide boosts to your stats, then an incentive is created for you to want to take ambiguous characters as allies, particularly if the stat boost they provide significantly exceeds that of other theme cards.
But wait, who said anything about stats? Well, one of the suggestions that emerged during playtesting was to give each player a concrete identity in the game world, and some stats and perhaps a special power or two. Certainly this will help communicate the theme if you have a well-defined persona, and the stats could also help with the strategic layer: since challenge categories are correlated with different location types, your starting stats might lead you to emphasize visits to one type of location over another, and correspondingly to build your information hunt around the theme cards that are also associated with those locations.