You can't be seriously claiming that self-signed PEM certificates were working well. I've been using them for years in various contexts, and they're an absolute nightmare.

Despite all their faults, for the average user, Passkeys are still miles ahead of GnuPG card, PIV, PKCS#15 etc.

Please check how the client certificate interface of Lagrange, the Gemini browser, works. It's nowhere as complicated as you make it out to be. No passkey interfaces I've seen is as clear as this one. It automatically provisions the certificate (optional. You can share certs among services if you prefer) and associates it with the correct service. So no complicated stuff. It prompts you at the correct time for permission in the clearest way possible. It's like an integrated password manager where your credentials are just files - sort of. That's all that a regular user needs to know about them. It can be exported, imported, backed up, synced, and what not.

Gemini strives to finish an entire request in a single transaction. So TLS certs are really the only option for authentication. That's how I learned the elegance of TLS client authentication workflow and started asking why this is so neglected in web browsers.