Hey there shmish,
Both look like fantastic bikes. I have 2 cross bikes. A Yeti Arc-X with road bars and a Gary Fisher Presidio that I converted to a flat mtb bar set-up. I honestly prefer the flat bar for urban riding scenarios. I just feel much more secure riding in traffic with a flat bar and having my fingers ready on the brake levers. I also prefer the flatbar for jumping pot holes and up and down curbs and aggresive urban riding in general. Sure a road bar is more comfy for longer distances.
As for braking system. I'm not a big fan of mechanical disc brakes, hydraulic are definately the way to go. Mechanical discs should still provide superior modulation and stopping power over Canti's or Vbrakes especially in the wet.
Just my 2 cents.
Yours in cycling,
LesMcLuffAlot