For all their faults these units are really good runners and even more importantly they mix really well with all the rest of my roster, Kato powered locos are robust mechanisms and I use them as the basis for a good part of my fleet. Units that can easily be programmed to run with each as a set of power are a big plus, so my Atlas units are a really important part of the scheme, I can run them with my upgraded '7s,'30s,'35s 45s and Genesis 40-2's. My Scaletrains T2's actually run a bit better than anything else and have a much different operating characteristic about them, so they run as a dedicated set, were they to take on early EMDs I'd still probably go for some, but maybe not - endlessly buying locos isn't part of my plans either.
I've got about 8 of them undec, which I wanted to turn 4 into MILW but the fuel tanks and frame have always held me back.
I'm in the same boat. I bought a bunch of undec GP40s and later GP38s because, in my mind, they were some of the first diesel models that stepped up from the traditional Athearn Blue Box line in terms of offering different prototype variations. I really only need a couple of each to build older CSX MOW "Pumpkin" units and maybe a Chessie survivor or two from the '90s.
The thing that really held me up was the shallow stepwells that were designed to allow the steps to be see-through but still molded as one part with the walkway. The middle step doesn't overlap (vertically) with the top and bottom steps as it should, and the overall stepwell is too shallow, if I recall correctly.
I really like that Athearn offered those fuel tanks separately. I bought a bunch, included a half dozen of the 4,000 gallon tanks to modify my Athearn SD50s, since CSX units have a slightly smaller fuel tank. Looking forward to see how those Rio Grande units turn out!
IIRC, the Red Box Atlas GP40 cab roof sides angle was off the prototype reportedly. I don't know if it's visibly noticeable. I have six of those Red Box D&RGW GP40's - four are unnumbered. Supposedly Atlas corrected the cab angles on cab roof on later runs - I think starting with the run that included the ex-Conrail GP40's.
If I remember correctly, the Atlas cab subbase is too tall, which raises the sides of the cab. The cab sides are still the correct height, and the roof remained at the correct height above the rails, so that fudged the angle of the part of the roof connecting the sides and rooftop. If you replace just the cab, with a Cannon cab, for example, the cab will sit too high because of the subbase. The best option on the early models is a complete cab / nose / subbase replacement.