That is something I do not see in my own (n=1) experience. The only problem I had was with a poorly written crontab entry, that was totally my fault.

Setting up my 5 domains, hosted on one small (virtual) server instance was just a breeze. Esp. compared to my former experience with StartSSL.

And now, with a cronjob doing auto renewal everything is solved. So for me at least Let's Encrypt just made life better.

This was also my scenario.. 10 domains, one virtual server..

It took me about 45 minutes from "never done this" to "all sites done with a cron job for auto-renewals".

The final thing I did once everything was set up was donate to the project.

Not even then. They should be using the staging servers for all testing and integration so they'll never hit the limits (a small server owner will not be needing more than 2,000 certificates per domain to be issued per week).