Where is the focus actually set in your pictures? You can evaluate this in camera (Menu - Playback Menu - Display Options) and turning focus point on. You can also evaluate in Nikons Capture Software (you have to buy a license for this, but I believe Nikon allows a free download and 30 day trial).
It could be that the focus is just getting set to the wrong place.
If that is the case, try other focus modes (AF-S with an external Speedlite, for example) which give you more control of the focus process and might yield results more in line with what you want.
Maybe you can upload one of these photos, with EXIF data preserved, so that we can see the problem?