I have wanted to go that step further and implement certificates for a good few years now, I absolutely see the value, no question about it (i.e. no more out of date authorized_keys files, no need to even install authorized_keys files in the first place, the list goes on).
I wish YubiKeys were more flexible in allowing SSH certificates to be hosted on them (currently can only host X509 type). Because if I could use a Yubi for SSH certificate signing I would have already been using certificates ! (Yes I know, theoretically you can do it with GPG keys, but frankly that's a PITA with many issues).
My current plan is to take inspiration from this : https://smallstep.com/blog/diy-single-sign-on-for-ssh/