And if you just rely on the default trust stores you’re actually introducing over 100 third parties, some of which are known to be controlled by (or at least work with) the NSA, China, etc.
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.