Several things. I can't use it for file encryption as well, and it's not possible to make a software key as backup (as far as I know) in case I lose both my yubikeys. With pgp I have a break glass key on an encrypted pen drive.

Also, with SSH it requires a recent version which is not on all the boxes I need access to.

It requires pin code entry for every authentication unlike openpgp where I enter the pin once and then I just touch it for every subsequent authentication. I like that because I use it not only for login but also for other stuff like root elevation.

And I think agent forwarding doesn't work with it. It's not really something I've looked into though as it's just not something I can use yet for the other reasons.

For now pgp is just much better for me, though I wish I could use it on the web as well.