Actually, there are scenes when you get to see Yoda's whole body. When Yoda is walking off with Luke's lamp beckoning him to come to his house, you can see his whole body walking. And of course when Yoda is balancing on Luke.

And I just don't think the CG Yoda looks right. I've said it before, but his eyes are just different. It looks like a relative of Yoda but not Yoda. There's so much soul in those puppet eyes. That was the only good thing about the PM Yoda was that his eyes were still pretty much the same even if he looked... well, crazy, there was still an inkling of that old magic.