I would run disc brakes. I foresee there will be much more disc brakes for non-MTB/commuter uses in the future. Better braking and you will save your rims in bad conditions.

Another advantage is if you have your bike built around 700C wheels, you can go back and forth between 700 and 650B without brake reach issues. Of course, there are other issues such as BB drop, but I wouldn't limit yourself to 650B. You can even have a thin 700 wheel for quick rides and the 650B for offroad/commuting.