Hi there, ISRG co-founder and current board member here. In brief, shorter lifetimes force people to automate (which, e.g., avoids outages from manual processes) and mitigates the broken state of revocation in the Web PKI. That latter point especially is what I understand to be driving the Web PKI toward ever-shorter lifetimes.
I actually remember the discussion we had in ~2014 about what the default certificate lifetime should be. My opening bid was two weeks -- roughly the lifetime of an OCSP response. The choice to issue certificates with 90 day lifetimes was still quite aggressive in 2015, but it was a compromise with an even more aggressive position.
Considering how many ACME clients are available today with all sorts of convenient features, and that many web servers nowadays have ACME support built in (Caddy, Apache mod_md, and recent Nginx), I believe that people who don't automate ACME certificates are the people who get paid hourly and want to keep doing the same boring tasks to get paid.
With the move to ever shorter certs the risk to letsencrypt having an outage is higher.
It would be nice to read more about what the organization is doing around resilience engineering so we can continue to be confident in depending on it issuing renewals in time.
Do you publish any of this? DR plans? Etc.
I don't mean for this to be a negative - really impressed by LE - but we've had a lot of Cloudflare outages recently and my mind is on vendor reliability & risk at the moment.