The Phantom Menace did use a puppet for Yoda. It's Attack of the Clones and Revenge of the Sith that went with CGI for him, because people actually complained about the puppet in TPM looking fake. Which I kind of understand, because with every other creature in that movie being obvious CGI, the puppet simply looked out of place.Yep, it'll be like Return of the Jedi's Henson Yoda vs The Phantom Menace's CGI Yoda.