I’ve got a hot take: Yoda should only appear once in the prequels, and it’s in his scene with Obi-Wan near the end of The Phantom Menace
Exactly! Whenever I’ve done prequel rewrites, Yoda has been exiled by the Jedi for dogmatic disputes. Only Obi-Wan (and Qui-Gon/Dooku) know where he is (Dagobah). That way, the ESB surprise is enhanced (instead of us laughing with Yoda, knowing he’s just messing around with Luke).
While it’d be impossible to totally cut Yoda from the three movies, one could chop him out in a three-in-one edit with some difficulty.