Another alternative is to support cross communication between email and this new protocol until it has enough users that supporting email stops being a priority. Then start offering new installations with email compatibility off by default until the majority of the users are on the new protocol, then keep email support only on lts releases and finally remove email completely. This way you avoid having to carry the baggage of email forever and having to support an old protocol full of backwards compatibility hacks. This is all in theory, in practice I doubt this will ever get close to replacing email.
That works pretty well for IPv6, doesn‘t it (actually, it does not)?
The problem with that approach is that as long as 0.01% still uses the old protocol, you can‘t get rid of it. And then you have a bag with the old and new protocol and maybe after 20 years you realize it‘s going to take another X years until you have at least some relevant adoption, as demonstrated with IPv6.
If one is ever going to „replace“ email it happens on top of the existing protocols and not as a replacement.
You make a great point. A very popular protocol or standard is never fully replaced. Either it continues existing next to the new thing (IPv4/IPv6) or gets an update while still having to deal with backwards compat (HTML, CSS). Whatever the case is we'll still be dealing with email in 20-30 years from now.