To state the obvious - the issue isn't one of room with a given brake but that the brake bridge is lower than optimal.
Given that the location of the bridge isn't easily changed you are of course looking for the brake with the least amount of stuff between the two fixed points - the brake bridge hole and the outer surface of the tire.
Given all that obvious stuff I'd say the newest Shimano brakes, both Ultegra and DA, have the least mount of stuff between the mounting hole and the tire. I could be wrong and some other brand might give more room but from my experience the newest Shimano gives the most room.
dave
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