I'd have rather they'd used a better puppet in the PT (With subtle CGI enhancements) but the full CGI Yoda was the next best thing. I'm just responding to comments that seem to be putting it on a par with Boss Nass for unbelievability.

I was dreading CGI Yoda going into the theatre, but when we all saw the first shot of him (This one of him giving Palpatine a silent quizzical look)...

... I remember thinking, wow that's Yoda, that's really Yoda! welcome back old friend. Of course the movie went downhill from there with Yoda's duel with Dooku being the low point.

It is true that if he had been a puppet, perhaps they couldn't have done that ridiculous duel but inability to perform stunts never stopped Lucas from having pensioners like Ian McDiarmid and Christopher Lee backflipping all over the screen.

I'm guessing the main problem with the TPM Puppet was that Lucas told the sculpters to make him 30 years younger. Forgetting that 30 is actually 3 in Yoda years, so they could've used the exact same puppet from ESB.