tie your physical remotes into MC. I have the Harmony Ultimate remote and the Hub and it controls MC wonderfully. It does take a little time to set up your mapping since MC is not included in the default list of apps, but once you get past that it is very simple to assign incoming actions from the Harmony directly to MC.
Happy to lend a hand if anyone needs.
Remote Buddy is available for iOS, Mac and even Apple TV which is pretty cool because it can AirPlay your desktop which presents some interesting possibilities.