How is the Nikon D5000 inferior to the D90?

I don't think that "inferior" is the correct term. Really they are targetted at different markets. The major advantage of the D90 is that it has an internal AF motor so can focus on any AF Nikkor lens. The D5000 requires an AF-S lens to do the same thing. Other considerations are more external control buttons and wheels on the D90 and higher shutter lifespan.

The one thing that the D5000 has that the D90 does not is the swivel LCD screen. Since I don't use live view at all, the swivel does nothing for me, but someone who uses it, especially for video may find it useful.