Remember that Vader used the Dark Side of the Force to remain healthy and even breathe on his own. E3 gives even more clues that Palpy could have far greater powers in this department
If the force lightning damaged Palpy, so that he looks like wreck, he would heal a bit with his immense powers over those 20 years, right? If it was because is sapped his strength, he'd "recharge" himself over the time. So Master Sifo-Dyas' again gives very probable explanation: Palpatine could not keep his masquerade while using his force lightning, the very raw emanation of the Dark Side - thus revealing his true form of deformed aged man, twisted by the evil corrupting him. Later on, as the Emperor, he had no need to cover it up with a mask of a "goodie-goodie senator".
P.S.: Do you believe he was actually hailing from Naboo?