I am asked with alarming regularity why I am not using Let's Encrypt for my personal Web sites, and for Adélie's site, and for my mother's art gallery site, and so on. "Why do you pay money for something you could have for free? And then you aren't giving money to those evil CAs!"
TLS certificates are still very much "you get what you pay for". Let's Encrypt is free, and on paper it seems to be a great solution with roots in freedom and socialism. However, it has a number of large issues in practice that prevent me from being able to adopt it.
The first, and most evident, is the failure of the community to provide a single ACME client that is well-supported and provides configuration options. As of this writing, there are 49 different client implementations on the official site. The problems with them are as numerous as the offerings; my main complaint is that most of them require themselves to run as the root user to automatically write to sensitive certificate files that are owned by the Web server user and are chmod 400.
The second large issue I've seen is that most of these 'automatic updates' break. This can be due to administrator error - and since there is not one single option, there cannot be a single repository of knowledge. This can also be due to APIs or endpoints changing. I have seen an official Mozilla blog and Void Linux's repository broken in the last week alone, all by botched ACME cron jobs. This solution is sold as "set and forget", but it requires more effort than simply going to a site every year and inputting a CSR and privkey.
Other issues with Let's Encrypt include: Let's Encrypt lacks a "site seal" which is very important on e-commerce sites to foster user trust. Let's Encrypt does not provide OV (let alone EV), which also compromises trust in people who know what to look for.
All in all, I think going forward Let's Encrypt may be suitable for power users and people who run TLS servers off their home servers. It may even be suitable for some personal sites and blogs. But I don't think it is a long-term solution for person who need trust, or those who have a complicated infrastructure (such as a distro, like Adélie).