> Also, I've never had a security issue due to TOFU, have you?
This is a bit like suggesting you've never been in a car crash, so seat belts must not be worth considering.
Do you feel that beyond the obvious and documented work in setting them up, there are disadvantages to using SSH certificates?
Your ISP or telecom has to be compromised for TOFU to be relevant to anything. In practice that never happens.
Certificates provide extra features, like revocation.
However, if you do not need the extra features provided by certificates, using SSH-generated keys is strictly equivalent with using certificates and it requires less work.
TOFU is neither necessary nor recommended, it is just a convenience feature, to be used when security may be lax.
The secure way to use SSH is to never use TOFU but to pair the user and the server by copying the public keys between the 2 computers through a secure channel, e.g. either by using a USB memory or by sending the public keys through already existing authenticated encrypted links that pass through other computers. (Such a link may be a HTTPS download link.)
When using certificates, a completely identical procedure must be used. After certificates are generated, like also after SSH keys are generated, the certificates must be copied to the client computer and the server computer through secure channels.