NVH = Noise, Vibration, and Harshness. This term comes up frequently when discussing automotive drivetrains but it's equally applicable here.
Your Atlas O SW switcher is the rare, rare exception; perhaps the only mass-produced O gauge diesel with a performance-oriented drive train. However its gear ratio is 15.3:1, which isn't really that low. Combined with the tiny and inexpensive Mabuchi RS-385 motor that Atlas spec'd for these, it's capable of speeds in excess of 70 scale mph. So this drivetrain would actually be better suited for a GP-9 or F-3. I spent two years trying to convince the folks at Atlas of this. But when the switcher was designed, Atlas was new to the 3-rail market. They didn't understand that most 3-railers care little about slow-speed operation. They soon realized that there was more profit and perceived marketing value in using two small, cheap motors with a big electronic sandwich in between. So unfortunately, the HO-style "cassette drive" in the SW was never repeated.
Another reason your switcher runs more quietly, is because the hood and frame are die-cast metal. There's a reason they don't make band instruments out of Zamak no. 3!
Given the small production runs, I imagine Scott couldn't afford to tool metal "gear cassettes" (like the SW has) for his 4- and 6-wheel trucks. So he went with individual axle gearboxes instead. This is a common and respected approach in 2-rail O scale. A "tower drive" such as this will be noisier, but an indirect advantage is that it's usually possible to change the gear ratio (more on that below.)
The advantages of a large, torquey motor combined with a low gear ratio go beyond sustained slow speed for drag freight. In a passenger loco, this combo has the potential to confer a much smoother start, especially the initial transition from stopped to moving. Think one... two.. three scale MPH with the slack stretched. For those who just turn their trains on and let them run, this doesn't matter. But for those of us who really operate our trains, nothing pricks the delicate bubble of realism like a jerky start. Reduction gears multiply torque, and the smoothing effect of the flywheel(s) is especially dependent on RPM. This transition is very hard to get right with closed-loop feedback electronics alone. (Look at some YouTube videos of Proto-2 diesels to see what I mean.)
Getting back to your issue... I'm willing to bet that 3rd Rail can change the pulleys in your loco specifically to give it a higher top speed. If you're still unhappy, and taking into account the size of your layout, you can probably afford the services of someone like this:
http://rodmiller.com/drives.html
For the rest of us poor folk with straightaways of 12' or less, slow trains make a short run seem longer. I reiterate that we would be better off if 3rd Rail and the other manufacturers geared their locos for a speed range of 3~60 mph WITHOUT the need for failure-prone electronics.
My post isn't meant as a personal diatribe, so please don't take it that way. I know Scott and reps from the other manufacturers read this board. The recent cab units from 3rd Rail could spark a revolution in O gauge dieseldom that's been 14 years overdue. I simply can't remain silent and see that spark extinguished by complaints, however well-founded, from a less well-informed minority. Thanks for understanding, sincerely. -Ted