I always just thought the Emperor was really old, possibly corrupted by power and the Dark Side, kind of like that guy in the Lord of the Rings while he’s under a spell, and that’s why he looked like that in ROTJ.

But given what happens in ROTS, there are two fairly convincing theories I’ve heard:

Palpatine had been disguising his “true form” somehow with some kind of force spell or something, and that was washed away by the lightning.
The lightning has a more damaging effect on Sith than it does on Jedi, or that it somehow takes a toll on its user that causes it to have much more severe impacts if it rebounds.