Steve Perry Offline Upload & Sell: Off
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It's really tough to see slight softness at web size, these don't look bad to me. Post a few 100% crops.
In any event, the images coming out of my D500 are very sharp - sharper than my D4 or D5 (due to the lack of an AA filter no doubt). I always need less sharpening on my D500 files.
Although - here's a thought...
There could be something wrong with your 400mm. Ostensibly that doesn't seem to be the case since you're happy with it on the D3s, however, the D3s has a much, much lower pixel density. The D3 is just over 5MP if you were to crop it to the D500 DX area (or the D500 would be a 48MP if it were an FX camera). That's a huge difference in density.
In a case like that, there's a possibility that a problem lens may look fine on the D3s but not so much when "stressed out" by the higher pixel density of the D500. (Note that the 400 2.8 should be tack sharp on the D500, it's never been accused of being a soft lens unless there was a issue).
I'd do some careful tripod-mounted, mirror up, live view tests with the 400 2.8 and eliminate any PDAF issues. If you can't get a razor sharp image that way, it might be a lens issue.
I'd also test the camera the same way with another lens. If both are soft, maybe there's something misaligned inside the camera (doubtful, but still a thought).
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