I've said it before and I'll say it again, in my opinion Yoda has no place in the PT at all. I don't think the audience in 1980 were meant to know his identity until it was revealed by Obi's voice, and in that respect, excising him from the PT entirely respects this reveal.
He should be spoken about a lot, building his legendary status for the audience, but we shouldn't meet him.
Obviously cutting all the shots he's in would mean there'd barely be a movie left, so why not replace him in some of them (the ones with the camera angles that indicate a short person) with another short character who can be given a new role in the story? Doesn't need to even be a Jedi. In fact it shouldn't be because that would again be introducing the whole "size matters not" thing prematurely. It could be a costumed dwarf either human or alien, masked or unmasked, or even a droid if the role could be made to fit the scenes with those particular angles.
Would this be enormously impractical and insane to attempt? Of course it would, and it's probably next to impossible. More insane than replacing CG Yoda with puppet Yoda? No, in fact without the need to....
1. Puppeteer
2. Sync the mouth movements to the existing dialogue
3. Impersonate Frank Oz's voice in the case of new dialogue
...it would be a lot easier. And there might even be a greater payoff due to the additional scope for changing the story with whole new dialogue from a whole new character. You'd only need to worry about matching the angles and/or motion (not that I'm downplaying how hard that alone would be).
I know many here disagree that there's any point preserving this reveal, or that it even was a reveal at all, but that's my opinion. I'm in no way suggesting this is doable anyway. This is just a 'what if'.
EDIT: Damn you muddyknees2000 and your incessant mind reading!