It's hard to see how this situation is any worse than CA1 simply issuing false certificates. If you can't trust your CAs, you're lost. Once again, if you can't trust you're CAs, you're absolutely hosed. Meanwhile, the general objection remains even there weren't a real example. Which, apparently there isn't, since none of your examples really qualifies.
Many systems have such errors but somehow manage to continue to work.
Like it or not, to the extent to which we have a certificate infrastructure, it's X.509. That's the kind of certificates that systems have and its the kind of certificates that software knows how to parse. Before we decide to junk all that, I'd like to be fairly sure that it has crippling flaws. Your argument so far isn't exactly convincing.