I know this idea has been thought of before, so I'll just ask how quickly it was shot down.
What if the Emperor on the Second Death Star was a clone?
This disregards the prequels, as Anakin/Vader would have known the difference, but if Vader of the OT had only ever seen the Emperor in holograms, how would he know if he was talking to the real Emperor on the Death Star? Also, the Emperor changes dramatically in appearance in both the original trilogy and the special edition, so it could very well be a rapidly aging decoy placed on the Death Star to test Luke and the rebels, as well as Vader's loyalty, without ever exposing himself or even risking a completed battle station. The Emperor's "Best Troops" seem inferior to even generic stormtroopers, perhaps implying that the clone Emperor wasn't aware of the real condition of his troops. The Imperial fleet flees after the battle, even after it still seemed to outnumber the rebel fleet. Was it an unexpected retreat, or a calculated move to make the rebels think that they won and lower their guard?
It's just that if the EU is going to be thrown out, why not go crazy? Everyone agrees that cloning the Emperor is a bad idea, but that's because the real McCoy was already killed off, leading to cheap imitations. But if Luke was overpowered and Vader killed by a cheap imitation of the Emperor, how powerful would the real deal be?