I think that somewere between ROTJ and TPM, Lucas forgot how to make puppets. Yoda in the OT was great. The puppet in TPM was terrible. There is no excuse for it.
As for the Emperor's look in ROTS, if you compare how Palpatine looks in AOTC, it looks like they started with the darkside corruption/rapid aging, then decided to shift to the goofy force lighting scarred him. He looks younger in ROTS to me than he did in AOTC. I don't see why they needed to have him get really old really fast for ROTS. Just have him look older still. After all, it was 25 years between ROTS and ESB. And the ESB makeup looks nothing like the ROTJ Emperor anyway. Did Lucas even bother to watch ROTJ before designing the makeup? Maybe that will be the next change. Making ROTJ emperor look like ROTS/ESB emperor.