How problematic is that in real life? All CAs worth their salt are already publishing all certificates to CT logs because most TLS servers are browsers and most clients are browsers.
Maybe there's a CA somewhere that has opt-in CT logging enabled, but I don't think they're very popular. For example, even the rogue CA certificates were published onto the CT log (because Let's Encrypt does so by default).
I think a CT check shouldn't be a very problematic change in practice, as long as there are reasonable exemptions (i.e. don't require CT for certificates imported into the CA store, allow the user to disable the check, etc.). For server<->server communication things become more difficult, but the entire network would be better off if a major server like ejabberd were to require CT.