Darth Venal said:

Digital Yoda will inevitably replace the puppet in The Phantom Menace in a future re-release. I just hope they don't replace the wonderful puppetry in Empire and Jedi. At least the Jabba puppet in Jedi would probably be too expensive and too difficult to replace completely with CG, so I think that's safe for the most part.

They already did that for TPM. I just didn't know they were showing it in public.

As for replacing the puppetry in the OT, I can only say that right now Lucas won't do that, and the current animation team at ILM will leave before they do that.