Allowing multisignature models would at least drop the single point of failures, by being able to require verification from multiple CAs. In combination with certificate transparency and DNSSEC+DANE it would add much stronger security.

I think the criticism was meant as one of the CA model, not Let's encrypt specifically - you have no choice about using CAs if you want to use https to serve a site to normal users. Also, I'm not the OP and think Let's Encrypt specifically is a great idea, already on the waiting list.