Be careful with a flat roof. One of your first calls should be to your insurance agent and see how much of a surcharge you are facing on your homeowner's policy with a flat roof. Up here in the great white north, many carriers will not insure a flat roof against the event of collapse.
For walls, if it becomes a choice between square footage or beefier walls, I'd vote for the larger area. We had the same choice when we built. We used 2x6 construction in our residence for structural & insulation concerns, but went 2x4 in the garage to free up a few dollars allowing us to go 24' deep instead of 22'.
Would I have liked 2x6 walls in the garage? Yeah. Am I happier to have the extra elbow room? Absolutely.