From a pure probability standpoint, anytime you add more components to a closed system, that increases the probability of a total system failure unless the added components function in a redundant capacity.

If anything in a separate brake system would fail causing you to lose air pressure then all that is lost is brakes. However if a component in a separate landing gear system would fail then you are out of luck anyway and it wouldn't matter if the brakes were part of the system or not.

If channels are an issue, the retract valve and a simple button valve (controling the brakes) could operate off of a single servo. Using a button valve just fill the brake tank to an optimum pressure.