Funny, I actually disagree with everything except your points about the suspension and knobby tires.
Weight - Add a rack, panniers/bag, lock, lights, fenders, etc to a bike, and the original weight of the bike isn't a big deal anymore.
Tires - There is little time difference between my road bike (700x23), MTB with 1.25" slicks, and MTB with 2.15" Schwalbe Big Apple slicks. For my every day 35 mile round trip commute, you can pry my Big Apples from my cold, dead hands. They feel a bit heavier when accelerating from a stop, but that's about it. The comfort advantage of getting to run them at 30psi and having them absorb crappy road surfaces is well worth it. Agree on getting rid of knobby tires though, slicks are the way to go.
Lighter wheels - No thanks, I'll take durable over lightweight. My road and tri bikes have light wheels, but they also don't need to go up and down curbs, hit potholes, and do whatever else I need on my commute.
Disc brakes - Not that much heavier than conventional brakes, and superior performance when it's wet or snowy out. I'd opt for a nice set of cable-actuated discs over hydraulic ones though, for ease of maintenance.
Drop bars - Personal preference. I have plenty of hand positions on my flat MTB bar with stubby bar ends. Ergon grips help here.
Overbuilt MTB frame - Overbuilt = durable. Q-factor? Again, why bother talking aerodynamics on a commuter, any gain you get from a narrower Q-factor goes right out the window once you start adding commuting bits like racks and fenders.
