Right, but that doesn't mean all puppet Yodas are bad. It just means that, in their attempts to make a slightly younger looking Yoda, they did an awful job. I think that replacing him with a CG Yoda for the Blu-rays is a great idea.
But, just like the Clones, that doesn't mean it wouldn't be appropriate to sometimes replace him with a good looking puppet. I'm just not sure it's feasible.