Decent movie, but much darker than the first one... Despite all the awful things that happened in it, The Bourne Identity was about Jason Bourne gaining his future. Supremacy was about him losing it. At the end, he no longer had one (well, he lost it at the beginning, but the movie was about him dealing with it). Which gives it a certain resonance (after all, what isn't lost in the end?), while at the same time making it a lot less fun.
I liked Identity better.
At any rate, I honestly hope they never make a third... I don't know where they could go from here without it being completely contrived.