should we pin non-self-signed TLS certs?

Much drama over at https://medium.com/@pepelephew/how-to-intercept-all-wire-voice-and-video-calls-13da1246675c#.aa9txx9r1 because Wire don't pin their TLS certs (and also don't seem to put their VoIP signalling over axolotl). AIUI this means that an attacker can load a fake CA root cert onto a device, serve up bogus DNS with a bogus cert, and happily MITM away. Given we support cert pinning for self-signed certs (on iOS & Android at least), should we also do so for CA-signed ones too?