As bad as I think the prequels are, I don't see any need to remake them or erase them from canon. They weren't an essential backstory when IV/V/VI were made, so it's easy enough to simply disregard it, and only reuse elements from here on out that work or are necessary.
For example, I could see them never mentioning midichlorians ever again, since they were never mentioned in the OT, and likely an all but forgotten concept by now given the state of the Jedi. Same deal with a lot of the PT, actually. Since the OT was made first, obviously the PT wasn't essential to telling that story, and won't be essential to telling the continuing story either. The only time it even matters is if something contradicts what is in the PT, which I don't see being an issue for the reasons mentioned. Just because the PT was executed poorly, doesn't mean that any mention of it would be bad anyway, so I don't even see it being a problem, even for the anthology movies.