To upgrade, or not to upgrade

If you're looking for a new toy, adding a speed light would probably increase your photo opportunities more than upgrading your camera body. My first dSLR is/was the D90 and I probably got it at around the same time that you got yours, and I enjoy nature photography also. An off camera speed light can help things in the shade come out of the background, and there are some off camera tricks that can really make your subject pop.

I've also found a good, sturdy tripod to be useful. It's low on electronics but it can make you long on night time landscapes and you can really take advantage of the "blue hour".