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Hi Markus, I have been working a little bit with Mavlink, Mavros and the Px4 Firmware and I think that what you said is a little bit confusing:
Mavlink is a communication protocol between a ground station application and an autopilot board. Mavlink does not require ROS to exchange messages between these two agents. In fact, you can use any autopilot and ground station you want without having ROS installed in your PC. On the other hand, if you want mavlink messages to be published/taken in/from ROS, then you need to run Mavros on your pc. In this case Mavros directly "talk" with your autopilot, using mavlink, and publishes/subscribes to determined topics.
About your questions:
1) I've only used the PX4FMU board with no companion computer, so I can't really suggest you which one is the best.
2) What do you mean by "controlling"? For safety reasons I'd say all the controllers (attitude, position, etc) should run on the computer/autopilot in your drone. You can "control" the drone remotely in the sense of changing parameters and settings, send commands, etc. In this latter case, I saw that WIFI can be problematic (delays, high packet loss, etc...), especially if there are many people around. You can use 3DR module, or maybe a Xbee.
3) I hope I answered this question in the above introduction.
4) Erle Brain is mainly composed by a raspberry pi, so you should have enough computational power both for autopilot and executing other processing (in fact Erle Robotics sells a onboard camera that can be attached to their brain).
Marco.
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