The major difference to me is the autofocus adjustment and the shooting mode.
On this camera Autofocus adjustment is triggered by a button on the front left of the camera (The A/F or M/F switch). Depressing the button allows you to adjust the type (Single, continuous or auto) by the command dial and the autofocus area by the rear wheel. Formerly there were controlled via a button on top of the camera. It is probably better but it will take some getting used to. Also I believe that you can change the method of actuating autofucus to the AF-L button on the rear of camera, but I haven't read up on that yet.
The shooting mode is now controlled by and extra dial on the left top of the camera. Both dials are locked by small push buttons. I like this.
On the shooting mode dial on the left of the camera are two user set modes (U1 and U2) which are useful. Select your preferred settings for say landscapes and action and then save them to each button via the menu. Really handy.
One thing I haven't got used to yet are the buttons to the left of the screen. Nikon have added a new i button so you can check camera settings on the screen. This is very useful. However, in their wisdom they decided to swap the two buttons which magnify and decrease the image on the screen. So I press what used to be the magnify button and decrease the image! Not so useful.
Another good feature is the Live View mode which allows you to take either movies or photos when viewing through the LCD screen instead of the viewfinder. On my D90 you could only use live view for movies.