IF you pin services to a key you control this mitigates the problem with bad guys obtaining bogus certs, BUT now you need to manage the pinning application to ensure it knows about any new keys before they roll into use. This may force you to compromise on your rotation schedule, maybe you'd prefer to use new keys for the new cert you're buying this week but alas the new app version is still waiting for Apple sign-off, so it'll have to be next year instead.

IF you pin to an intermediate key, which is under the control of a CA, then bad guys who obtain certs from that intermediate will not be inconvenienced by your pin, but these keys are intentionally long-lived (they are protected in an HSM) so the rotation issue isn't as fraught.