The fundamental practical problem with the Certificate Authority model
Let's start with my tweet:
This is my sad face when people sing the praises of SSH certificates and a SSH CA as a replacement for personal SSH keypairs.
There is nothing in specific wrong with the OpenSSH CA model. Instead it simply has the fundamental problem of the basic CA model.
The basic Certificate Authority model is straightforward: you have a CA, it signs things, and you accept that the CA's signature on those things is by itself an authorization. TLS is the most widely known protocol with CAs, but as we see here the CA model is used elsewhere as well. This is because it's an attractive model, since it means you can distribute a single trusted object instead of many of them (such as TLS certificates or SSH personal public keys).
The fundamental weakness of the CA model in practice is that keeping the basic CA model secure requires that you have perfect knowledge of all keys issued. This is provably false in the case of breaches; in the case of TLS CAs, we have repeatedly seen CAs that do not know all the certificates they mis-issued. Let me repeat that louder:
The fundamental security requirement of the basic CA model is false in practice.
In general, at the limits, you don't know all of the certificates that your CA system has signed nor do you know whether any unauthorized certificates exist. Any belief otherwise is merely mostly or usually true.
Making a secure system that uses the CA model means dealing with this. Since TLS is the best developed and most attacked CA-based protocol, it's no surprise that it has confronted this problem straight on in the form of OCSP. Simplified, OCSP creates an additional affirmative check that the CA actually knows about a particular certificate being used. You can argue about whether or not it's a good idea for the web and it does have some issues, but it undeniably deals with the fundamental problem; a certificate that's unknown to the CA can be made to fail.
Any serious CA based system needs to either deal with this fundamental practical problem or be able to explain why it is not a significant security exposure in the system's particular environment. Far too many of them ignore it instead and opt to just handwave the issue and assume that you have perfect knowledge of all of the certificates your CA system has signed.
(Some people say 'we will keep our CA safe'. No you won't. TLS CAs have at least ten times your budget for this and know that failure is a organization-ending risk, and they still fail.)
(I last wrote about this broad issue back in 2011, but I feel the need to bang the drum some more and spell things out more strongly this time around. And this time around SSL/TLS CAs actually have a relatively real fix in OCSP.)
Sidebar: Why after the fact revocation is no fix
One not uncommon answer is 'we'll capture the identifiers of all certificates that get used and when we detect a bad one, we'll revoke it'. The problem with this is that it is fundamentally reactive; by the time you see the identifier of a new bad certificate, the attacker has already been able to use it at least once. After all, until you see the certificate, identify it as bad, and revoke it, the system trusts it.