I do shoot raw, but due to computer issues when I first got the D90, I didn't download the free trial of NX2 (5 days left on it). Photoshop and NX would not support the raw so I was shooting raw + JPG, just so I could view/work on pictures. I love that NX2 keeps the camera presets.
Shooting mode--I usually don't use the scene selections. I shoot in A or M mode, so maybe that is where our disagreement arises from. With the control that is possible in those settings, I feel that I can handle all the types of shots that come my way. I preset my camera to the baseline of what I like to see in the final picture and then tweak from there. For example, I have custom set the black and white mode to increase the red channel, which shows the black and white picture differently, because I like it that way, and I am happy with that result nearly everytime.