I had experiences with the both of them and I'm using WHM Auto Pilot now... know why? B'cuz it is 100x easier to handle, more user friendly, and doesn't take the resources taken out of your server, aswell as you are not required to go through a bunch of tutorials in order to get your client management running ;)

Although MB might have extra features, I still recommend WHM AP because soon it will have most of those features too and I dont think MB is the worth the money.

Which one do you prefer and why?

WHM AutoPilot 10/10!