The TPM Yoda puppet has been replaced by a CG one like in AOTC and ROTS, it just has not been released to the public on DVD yet, but there is a brief snippet of it on the ROTS DVD so that argument is a moot point now. But if you were stuck in a swamp for several years, some different you would look! Plus I don't think Palpatine looks so different in those two comparison pics you posted. You also have to remember Ian aged over 20 years since the make up was last applied by a different make up artist, and in ROTS he is seen unhooded and in many differing lighting enviroments as opposed to being stuck pretty much in the throne room in ROTJ. Whatever differences there were in the Emperor's face from ROTS to ESB/ROTJ could easily have come in the 20 some years between the movies.