Let's Encrypt
pros
- Works on any domains
- You can put an expiration update on cron
Minuses
- Validity - three months
- Requires the addition of an intermediate certificate
Cloudflare
pros
- Duration - 15 years at once
Minuses
- Works only on domains whose NS are hosted on Cloudflare
- It works only when domain caching is enabled (orange cloud in the DNS CloudFlare). Not very convenient in the development of the site, you have to put the Development Mode in the Cache section
- Requires the inclusion of SLL mode "Full (Strict)" in the section Crypto
- Requires the addition of an intermediate CloudFlare certificate to the generated site certificate. Read more here.
However, from personal experience, if the domain is hosted on CloudFlare, I use the CloudFlare certificate. I got used to the minuses, and the lack of a headache with updating the certificate outweighs these minuses, in my opinion.