After owning D200 and D300 with similar menu setup, I love the control and versatility it offers and do not find this menu setup cumbersome at all. Since these cameras don't have any preconfigured scene modes, it offers a useful way to configure your camera very closely to your most common shooting situations.
There are 2 independent banks. Each has 4 sets of settings...
Shooting Menu Bank has settings which largely relate to the way the image is processed during and after capture by the sensor. I.e. mostly data related settings. Hence settings for image quality, bit depth, compression, ISO, Noise reduction, Picture modes, white balance, HDR etc. I have mine set up as A=normal light, B=low light handheld, C=low light supported, D=HDR.
The Custom Settings Menu Bank contains all the settings for functions that aid in acquiring and capturing the image. i.e. mostly related to control of how light gets onto the sensor in the first place. Hence exposure compensation, bracketing, flash, autofocus, shutter release methods. I have mine set up for A=Normal, B=Wildlife/Sport, C=Macro, D=Landscape. Other options could include setups for portraiture, flash, night photography etc.
Combining a the type of subject with the ambient lighting/shooting conditions gives up to 16 different camera setups. The advantage of this is that it reduces the amount of fiddling and fine tuning for each new shooting situation that arises. On arrival at a scene I wish to photograph, I assess the conditions and type of subject and then make two menu choices - one for Shooting menu A,B,C or D and the second for Custom settings (A,B,C or D again). Then Voila! - with just two settings my camera is about 95% ready forthat situation. After this preparation, it is most commonly aperture, then focus (AF-C/AF-S) and then ISO settings that I would change manually during shooting.
It is not necessary, nor ever intended by the designers, that A should always correspond with A, B with B and so on.
One day I will take the time to write down and post details of these ettings - at this stage I am still fine tuning them.