I read the federal government’s Zero-Trust Memo so you don’t have to

TOTP is not going anywhere for much of the Internet. Hold on while I get a Yuibikey to my dad who thinks "folders can't be in other folders" because that's not how they work in real life.

TOTP is a great security enhancement, and while phishable, considerably raises the bar for an attacker.

The fact that TOTP is mentioned as a bad practice in this document is an indicator that this should not be considered a general best practices guide. It is a valid best practice guide for a particular use case and particular user base.

Yubikeys aren't the serious long-term alternative to TOTP; software keys embedded in phones are what we're going to end up with.