It is a rather limited protocol. Really, the implementation isn't so bad... In a perfect world.
It's naive.
It imagines there was a whole different set of operating circumstances at shared web hosts than the reality exhibits.
I actually had not read the protocol specification for that challenge as I utilize http-01 and dns-01 on all my various systems. Then, when the early report without details was released, I read the protocol and realized almost immediately that there were several circumstances in the field which could yield actual vulnerability.
They also made the mistake of failing to align to a promise which the other mechanisms do make: the other mechanisms tie the validation directly to the target domain label being authorized or a known child thereof. The TLS-SNI-01 and TLS-SNI-02 don't do that. And they knew that, because they wanted to be able to perform a TLS-SNI validation without having to change server software. I believe that was a bad decision.
The proposed TLS-SNI-03 ALPN "acme" extension that Mr. Rudenberg has put forth will not be resilient to these attacks, ultimately. I think they should do a real ALPN protocol and do the validation through that. But let's assume time to market for that would exceed a year. In the mean time, people reliant on TLS-SNI-01 are likely going to need to do something else.
In short, a mechanism which would achieve much the goal of getting validation off of a single TLS port running the right software can happen, but I believe it should borrow pretty much nothing from the current TLS-SNI-0x proposals.
It should be a whole new real ALPN protocol.