I hear the 5900 is much stiffer/lighter. 5500 more compliant/heavier. Just depends on what you want. I think that Trek should have Lance's new bike coming out soon? Why not wait for that..
As well as the frame, there's also a difference in wheelset and other misc. bits. I guess it all depends on if those benefits are worth the extra US$700 to you..
I know that either one would be completely wasted on me!