We've migrated from Yubikey 2FA to the university's MFA
We have a sensitive host that absolutely has to be protected with multi-factor authentication. When we first set it up in late 2016, the second factor we chose was touch-required SSH keys held on Yubikeys. Recently, we have been switching this host over to the university's institutional multi-factor authentication. The university's MFA uses Duo, so our sensitive host is set up to use Duo's PAM module.
(Integrating Duo with OpenSSH led me to explode what combinations of authentication methods we could and couldn't support with PAM-based MFA.)
Relying on the institutional MFA has some failure modes that using Yubikeys doesn't, since verifying Yubikey SSH key authentication is entirely contained on the host. However, we decided that we could live with these additional failure modes because using the institutional MFA had some significant advantages for us. I can boil these down to three general areas: availability, usability, and manageability for the people involved.
In terms of availability, institutional MFA has the advantage that people already have to routinely use it for all sorts of things, so they had it set up, working, and ready to hand. Our Yubikeys were only ever used for this host, so if you didn't log in to the host for a while, they could wind up not so available and ready. And in general our Yubikeys were yet another thing for people to manage and keep track of, like an extra and rarely used key.
In terms of usability, the institutional MFA is a lot easier to get going and work with for SSH logins, because all it demands from your SSH login session is that you type extra text. Yubikeys required a USB connection and appropriate software to connect to the Yubikey in either your SSH client or your SSH agent. Not all things that can run a SSH client even have USB, and of the computers that do, often the software was an issue.
(In the future, OpenSSH's new(ish) support for FIDO/U2F may help some of this, but only for things that wind up running OpenSSH 8.2 or better. In practice this means it will be years before Windows, macOS, iOS, and Android SSH clients can all reliably take advantage of it.)
In terms of manageability, the institutional MFA has other people who handle all aspects of enrolling people, managing their devices, recording the necessary data for server side authentication, and so on. With Yubikeys, all of that was on us and it wasn't necessarily a smooth and easy process. In fact it was so friction prone that we would never have scaled it up beyond the small group of people who needed to have access to this sensitive server.
The Yubikey solution was simpler, theoretically more reliable, and potentially more secure (and certainly more under our control) than the institutional MFA system is. But in practice both the ease of using and the ease of managing whatever we used for MFA turned out to matter quite a bit, and Yubikeys weren't really good at either of these. Institutional MFA is good enough, it's officially blessed by the university, and it's much easier for everyone to deal with, so it wins in practice.
(I admit that the Yubikey SSH key generation security issue soured me on really trusting some parts of the theoretical Yubikey advantages and shifted my views on where I should generate keys, as well as making me kind of unhappy with Yubikeys in general.)