Now, I might sound insane, but the only moment I found the CGI Yoda to look like a puppet is in ROTS, when he is figthing with Palpatine and he falls and grabs into that senate booth thing, there's a 2 or 3 second shot showing Yoda from a distance, trying to hold himself into that thing, he looked like the ESB puppet during those 2 or 3 seconds.