How can we fix a bug in the ACME protocol?

Let's Encrypt already has challenges making changes in full compliance with the ACME RFC; making further changes to the actual spec at this point would cause even more pain. (And it may be that the pain would be worth it, don't get me wrong, but I think it'd have to be a pretty high bar to be worth standardizing and going through the effort to get servers and clients to change their behaviors.)