I was writing about EtM constructions before Moxie wrote that post (you can see me preening about Bellare and Namprempre in Twitter search), but Moxie's post is the one everyone remembers, so that's the reference. What's "obsolete" about the advice now is that nobody builds cryptosystems by manually gluing a block cipher mode to a MAC anymore. But in the 5 years prior to that post, violations of the "principle" were the most reliable way to break cryptosystems.
Nobody's arguing that cryptographers can't design hermetically sealed authenticated encryption modes that play with the ordering of encryption and authentication. That wasn't what Moxie was implying either.
I think that you might confuse IPsec with SSH in this statement.
IPsec chose since the beginning "Encrypt-then-MAC", which is proven to be secure with any good encryption and MAC algorithms.
In the beginning, SSL used "MAC-then-Encrypt". This is proven to be secure only with certain combinations of MAC and encryption algorithms. Nonetheless this was not a problem for SSL, because the combinations that they used were by chance among those correct.
SSH used in the beginning "Encrypt-and-MAC", which is the worst choice, and in certain SSH variants it was actually vulnerable.
So I think that you remember some story about SSH, because IPsec got it right since the beginning.
In general IPsec has never had any problem in its purely cryptographic design choices, but its initial variants had ridiculously complex management methods, which could result in security problems due to key or access rights mishandling.
Later, IPsec was simplified, but it had already acquired a bad reputation as being extremely hard to use correctly, which allowed other VPN solutions to become much more popular, like OpenVPN, which were much easier to configure and use.