I skimmed the whole tread.
Mike Hearn's FAQ helped explain the reasoning behind this:
PKI is hard apparently.
I think the hostility to this stems from the fact that the CA system is known to be broken. An attacker will not try to change the "common name"; they will change the payment address: the very thing being hidden by this proposal.
With money on the line, attackers may even be well-funded, purchasing one of those corporate CA spoofing appliances in order to go after a high-value target.
I was also wondering why it was stated as fact that self-signed certificates allow the MITM attack. Later in the thread, somebody even pointed out that CAs themselves use self-signed certificates. The difficulty, hinted at in
this link is that X.509 certificates do not allow the end-user to trust a specific CA for a specific domain. All CAs can sign for all domains: which makes me trying to be my own CA for *.economicprisoner.com a very bad idea.
In my experimentation with OpenPGP, I noticed that most people have shockingly lax certificate verification practices. They are confused when you ask for their public key: when you can simply search for their e-mail address or their short-key is included in their mail signature. They don't realize that it is trivial to generate collisions with both of those identifiers. There has essentially been a gentleman's agreement to not do that as far as I can tell. This tells me that even if a "bricks and mortar" business had the fingerprint of their self-signed cert prominently displayed: nobody would actually check it.
PS: To the people hung up on SSL: You can have Certs without using SSL.
TL;DR: I still don't like it, but don't really have a better suggestion at the moment. Namecoin would not work since the first person to grab a specific .bit domain can not be forced to surrender it in the event of a trademark dispute (unless you can get the holder in court somehow).