This is only my opinion, and I don't speak for ISRG / Let's Encrypt - I'm just a technical advisor.
The reasons I can think of to start with the automatic client are:
- An automatic client is hard, hasn't been done before, and demonstrates the novelty and power of ACME over traditional methods.
- Most people who configure Apache or Nginx do not know what a CSR is. Or how to protect the keys.
- Personally, I want to never have to explain to people what a CSR is again, or how to generate one.
- Also personally, but specifically about CSRs: PKCS10 is IMO an example of everything that is wrong with crypto today.
Really, I expect someone's working on one right now, somewhere. Walk people through the OpenSSL commands to copy/paste, responses to copy/paste, toss some tasteful advertisements for Debian on there, and bam! I'll link it from the List of Client Implementations and someone will post it on Hacker News, and people will go to down.