I strongly prefer full length housing on top for several reasons. Makes picking the bike up easy. It is away from the top tube mounted pump. It looks clean. It goes a long ways to toward making the rear brake less effective and therefore a better match to the front. And there are fewer cable housing ends to introduce rust and other issues. (With full length cable housing, the only open cable end is at the brake, pointed down. If you ride with fenders, the greasing you do when you set it up last a long time.) Oh (edit), the cable is far less subject to damage and kinking as well.

Ben