I'm not claiming these risks are that significant, but given that LE takes just as much time and effort for initial set-up as a standard multi-year cert, if not more, I think the mantra "some risk of failure is more risk of failure than no risk of failure" is something worth baring in mind.
And I'm not convinced having 90 day certs is a huge security win. Not only can someone do a lot of damage in 90 days, but your private key (the important bit) can't be rolled every 90 days anyway without integrating your rollover scripts with your HPKP config. If you botch that then your visitors can't come back to your website until the pin expires. Scary. Site ending scary. And if you're not using HPKP then i'm not even going to debate the security pros and cons.
On remembering to renew certs... there are many many services out there to send you reminders. Pick 2 or 3 and use them all. Or use a CA that sends reminders.
I'm glad LetsEncrypt exists, but let's not treat it like the be-all-and-end-all.