Because we are introducing a third party into a situation that didn't require a third party.
For service-to-service stuff and APIs the number of TLS clients that respect pinning is approximately zero.
Either way, the other problems remain, and running an internal PKI is really pretty easy.
Also, using Let's Encrypt doesn't stop you from certificate pinning.
There are far too many ways to self-DoS accidentally with HPKP. Also, an attacker who briefly gains control of your public DNS or web server can DoS a hostname semi-permanently.