It was very controlled and effective, whereas the CG yoda just seemed like an animator's show off toy.
To me, it just screamed, "Look at his mustache hair! Look how it moves! Look how every square inch of skin moves whenever he does something simple like move his arm! You can't do THAT with a muppet!"
To show I'm not a total CG bigot, let's take the example with Gollum: the greatest CG character created thus far in my opinion. No fucking way could this character have been pulled off by a puppet. What stood Gollum out from the rest was the fact that they paid such close attention to intricate details like a slight shift in eyes, the lighting, his movements. Because of this attention to detail, they made a believable character (c'mon, who didn't cry when he had that talk with himself when the others were sleeping?).
With yoda - and this is the case with a lot of the SFX in the PT - it all seemed like effects for effects sake. It was cold and distant. it didn't fit in. It was all so rushed, so fake.
By the way, can someone explain to me why Yoda's english is better after 30 years of exile on Degobah?