Kinda funny to call the current 90 day certs "long lived". When Let's Encrypted started out more than 10 years ago most certs from major vendors had a 1 year life span. Let's Encrypt was (one of) the first to use drastically shorter life spans, hence all the ACME automation effort.
To someone like me with hobby-level serving needs, the 90 day certificate life is pretty inconvenient, despite having automation set up. I run a tiny VPS that hosts basic household stuff like e-mail and a few tiny web sites for people, and letsencrypt/certbot automation around certificate renewal is the only thing that I seem to need to regularly babysit and log in to manually run/fix. Everything else just hums along…
On the top of my head, that could be because one or more domains are not accessible from the public Internet (which could be for a variety of reasons), a subset of the subject domains having expired for legitimate reasons but you might not know which in advance (certificates being what they are some application rely on them having alternative names), intermittently flaky routing (which might not be a problem for the application), and a number of other reasons. That's without including potentially hostile actors. Then there are plenty of offline uses for certificates!
That said, Let's Encrypt has really been a revolution and made life better for many people. But it's not perfect and the PKI system itself has many warts. It's absolutely a system that may need a non negligible amount of babysitting when you venture outside the absolute mainstream.