> 1. Still WAY too complicated (look at all the stuff you have to know and type)
The website mentions at the bottom that they're intending to get all of this automated, but they're not at that point yet; they're still in public beta. Certainly all those commands look automatable, just with enough integration with lots of distros / web servers, testing, and debugging. The Let's Encrypt protocol (ACME) is very much designed so that a web server can acquire a certificate with just about no human interaction besides telling it to do so, and keep it up-to-date with no human interaction.
I certainly agree that the instructions on that website are still way too complicated for general use, though far, far simpler than the status quo ante Let's Encrypt.