Sorry, my English is not so good so sorry if it's like I blame Let's Encrypt 
I have a project with 100K domains so I hit the limit very fast, and I'm using Caddy to take care of everything so I don't deal with that.
Anyway, I'm not blaming Let's Encrypt, I'm saying that the internet needs to be LIVE 24/7 and all the SSL projects make things very difficult to manage because of that rate limit. Not all developers have the same knowledge in the SSL field so things need to be much easier so the internet will not be broken.
The reality, there is not a lot of good commercial solution in the ACME field because of the Let's Encrypt free solution (no one wants to compete with free alternative), so I think Let's Encrypt need to understand it and offer a better solution so the internet will not go down.
Increase limit from 300 to 1000 is just a plaster when you don't know how different customer is affected.
I hope I explain my situation better now (and again sorry for the English)