I also suspect it was just ease of convenience. Which of course, it is. Just look at the BTS of Empire. Most of the Dagobah set was Frank Oz walking beneath the platforms, obscured with the fog. Plus, it was difficult for Hamil to hear what Oz was saying from below and had to rely on, if I remember correctly, screens to show Oz speaking and then Hamil would know when to say his lines.
Now you’ve gotta use more Yoda, under the vision of Lucas, in the PT. He wants flippy Yoda? Gotta ditch the strings.
Definitely, CGI was the way to go for the things Lucas wanted to do, it just struck me as odd with how different the character looks from its puppet design