Https is worse from a usability standpoint because of the need for trust stores and keeping them up to date. While it's mostly taken care of by the browser, it can still cause problems when you don't have anything in your truststore that can verify the other certificate.
Ssh vs rsh suffers a similar problem. If the certificate on the other side changes, you have to update your local config to allow the new certificate and will either be blocked or have warnings until you do so.
Pretty much with anything that requires certificates, usability is worse because you have to maintain the trust store in some way.
In both cases you mentioned the effects are very negligible and certainly worth the tradeoff, but strictly speaking, the usability is worse.
> I can't think of a single counterexample where security did not have an effect on usability.
Sticking with the "mutually exclusive" criterion, wouldn't ssh vs. rsh serve as a counterexample? How about https vs. http?
Both replacements brought us greatly improved security, with no effect on usability in the vast majority of time I've spent with them.