And that's a big downside of the low certificate lifetime.
I guess that the most websites, we can find on the web, are hosted on some kind of "shared hosting". Only very few websites are hosted on "root servers".
So if the goal of the whole "letsencrypt" project is really to encrypt the whole web, then you have to allow longer lifetimes optionally. If someone can run the client, then 90 days should be OK, but on my hosting, everything, I have, are two text boxes to paste the content of the key files. I can do this as often as I want, but manually generating a key every few weeks and uploading it via web GUI would just suck. This way, I'll prefer to not even start with HTTPS.