What? This just sounds like you're doing it all wrong then blaming the tools.
Maybe I'm just thinking about it from my POV as a mainly hobbyist user of SSH, but I rotate my keys (not as frequently as I should, but I do), and I remove old ones from .authorized_keys files and I use different keypairs for different servers sometimes too. I never copy keys to other devices - I ssh-keygen on every device, and add my pub key to the authorized_keys file manually.
It isn't even "hard" to do it this way. Sure, it doesn't "scale" for big corps - but I don't need it to scale, so I'm not "doing SSH wrong" by not using certificates.