Well, it appears as though the Company already has plans to merge Pirates of the Caribbean and Splash Mountain into a new HKD hybrid ride called Pirate Mountain.
At Disneyland, I think it would be way cool if Jungle Cruise and the Indiana Jones Adventure were to be connected.
I envision the Jungle Cruise becoming an excursion with the purpose of meeting up with Dr.Jones. The current Indy queue would connect with the Jungle Cruise instead. Your skipper would periodically interact with Dr. Jones via an Indy era walky talky. The cave at the end would be loaded with special effects. At a point within the cave, guests would depart their boat, and climb into a jeep. The adventure would then continue pretty much as it does now.