I actually think they're better in TPM and ROTS than in the middle one. Call me nuts but Attack of the Clones was the least convincing - they were still new at doing Yoda, a lot of the environments sucked. In TPM they had enough practical stuff to make it look good, and in ROTS they finally had ironed out their problems. Heck, in the shot where Yoda goes "consumed he is by Darth Vader" I was finally able to think 'hey he looks like a puppet'.
And you don't know how much I hate CGI and how much it pains me to credit it. So trust me, by ROTS it wasn't that bad.