I think the reason why some people want the CG Yoda is that they just want something different on these disc than what is already out there. Also, as much as I hate CG, that puppet just never looked right. I extreme difference in Yoda's look between Phantom and Clones is almost as jarring as the difference between his look from ROTJ and TPM. I still don't understand how that puppet went so wrong...
The bottom line is, the version of TPM with the puppet is and always will still be out there. I have said it many times, I have no problem with special editions or director's cuts, but I really want to be able to see it the way it was originally seen. As long as that original version is out there for me to enjoy, I have no complaints (which brings us to the fact that the original, and to me much preferred version, of The Phantom Menace is not out there on DVD, which, as much as I hate the PT, I still find unfortunate). So I do not think it is at all wishy washy of some people here to wish for this change.