The D90 is technically a better camera but it's not all better. If you only use it in an underwater housing, then the D90 is the obvious choice. But other than that, the D200 has some more advanced settings that the D90 lacks, it has also much better ergonomics and more buttons (which most people prefer, less fiddling in menues). The D200 also has better (more correct) colors in its jpgs. The D90/D300 and I think also the D3 and D700 has problems with its jpegs. Especially with the color red that is over saturated etc.
So, for a land based camere there are many pros / semi-pros that consider the D200 to be better than the D90.
Hmm I think the D200 has more focus points too, not sure though... I love tons of focus points (my D300 has 51, I just wish they were all cross points...)!
Yes, noise level is lower on the D90, but it's not that much. It's nothing like a D700/D3 (D3s ;-)).
I would anyhow recommend you to go for the D90 as it has a much better display and can do video.
But, on the other hand, I think you can get two second hand D200 for the price of a D90. And if it's something I really miss having (I have currently a D300), it's an extra camera housing when travelling. Either you get two D-SLR housings or you have to buy a complete extra compact system (which will not be cheap and will always be less good).
Hmm why do you even consider upgrading to a D200? If you want a more professional camera body, the D90 wont give you that. If you want a camera that takes better pictures, the D90 will hardly give you that either. If you want a better display, live view and video features, then go for the D90.