I have a good line of Nikon DSLR's, starting with a D70s (which is the only one I sold). D200, D300, D700, D800e, D810.
The first thing that bugs me about all of them is the 'bank' system for holding settings. Frankly I've never understood why the settings are split into two banks, but the real issue is that you can't be sure the settings you want are saved. Reason is, any change you make is automatically saved, so if you pull up a banked setting, then make a change while shooting, you've just altered your banked setting. Plus you can't set all the settings into a saved mode either (like returning to RAW mode). The lesser, non-pro, models have a U1 and U2 system (two user modes) that is pretty much correct. Not so the Dxxx series.
I have a bit of gripe that the eyepoint on all of the above cameras isn't high enough. I shoot with glasses, and a higher eyepoint would be nice.
The D700 and D800e do have a pretty noticeable shutter sound. Didn't notice it that much until I got the D810, which is much quieter.
Bracketing could be better, in that you can't set very extreme limits. I guess that applies mostly to HDR shooters, but with the dynamic range of the 8xx sensors, that doesn't seem so needed.
I don't like the slow frame rate on the D800e. It's better (surprisingly so, since it's only 1fps better) on the D810, but I had 8fps on my D300 and D700.
The menu systems on all the Nikons are a bit quirky/busy. Thom Hogan nails it on his comments along these lines. There are entries you might use a lot that are buries in menus, and other things hardly needed after day one that are near the top.
Nikon's software .... argh.
Having started shooting Nikon in 1992, I'm awfully used to the way the cameras are laid out, so may not even see some quirk as a quirk anymore.
Trying to think of stuff about the cameras that causes me waste of time or annoyances - really the one big thing is that I can't just hit some menu option to reset the camera to a known state, which is the job of those settings banks.