Hmmm....this is a tough one. It has to be archeological, supernatural, and potentially offensive.
Firstly, it will probably be Judeo-Christian since Lucas won't really care about offending Hindus, Buddhists, etc.. Plus, he, like most of Hollywood, doesn't want to offend Muslims, so Islam is safe.
The "Bones of Christ" idea sounds interesting, but I'm kind of stumped on what the supernatural aspect would be. The Indy universe has established the existence of "holy" magic, so negating the resurrection would be kind of strange (and make the Holy Grail from Last Crusade look questionable). Plus, I've never heard of any "bones of Christ" legends with which to draw supernatural elements from.
He could go the God Told Me To route. That film tied to virgin birth to UFO abduction. Jesus was an alien hybrid and God was nothing more than a UFO. While that would certainly offend people, it isn't very supernatural.
I doubt it's going to be a descendant of Jesus or the next Messiah since I'm not sure about the archeological aspects or how The Last Crusade fits in.
I'm seeing a pattern here. If it's something to do with Jesus, it can't contridict the Holy Grail.
Also, I kind of doubt The True Cross or Spear of Longinus theories since they don't seem that offensive.
The Anti-Christ idea would fit in the Indy universe. Perhaps he'll reveal that it was Hitler? Hey, wait a minute! Indy kills the Hitler Anti-Christ! Yeah, Hitler wasn't cremated, he burst into flames when he died!
