There's also a lot of "junk" between the trucks, fuel tank and sill that is absent on the model. Frame, air pipes and wiring runs. This isn't helping matters. Mike Danneman had a good article in NSR on fixing the same problem on the IM tunnel motors. This greatly improves their looks. The trucks themselves would benefit from some extra detailing, especially the prominent air line connecting the brake cylinders. If you take it a step further, you could add a lump to the end of the trucks to represent the traction motors. Anything to help fill the "dead air" down there.
The Atlas SD50/60 fuel tank is also fugly. There's not a lot of depth there, especially around the air tanks, and the metal frame halves are visible on the ends. At least paint those black.
All of these things can be easily added with some pretty basic modeling effort. Not much you can do about the thick sill, unfortunately. But the model can be made to look better by adding some details below the sill.
Pete