Well, it wasn't awful. But it wasn't great either. After much pondering, I reached the conclusion that the reason wasn't the plot or the action sequences or Matt Damon. The problem was the lack of a strong antagonist and a strong alter-ego.
In both the first and second movies, Bourne has both a strong antagonist and a strong alter-ego. The antagonist is the mastermind behind the current movie's CIA operation. The alter-ego is what or who Bourne would be if he hadn't woken up/broken his training.
In the first movie, the antagonist is Chris Cooper, one of my favorite actors, and a guy with effortless charisma. He has a number of factors in his favor, including his grim resolve, his investment in Treadstone, his disgust towards his superiors, and his lack of fear (he doesn't fear Bourne, for one thing). Bourne's alter-ego is Clive Owen, who also bubbles over with charisma. His scene in the field outside the farmhouse with Bourne is powerful. His characterization as the "hit man" that Bourne used to be is vital to this and the later movies, especially since the Professor (Owen) is willing to give Bourne information.
In the second movie, the antagonists are the cool Joan Allen and self-protective Brian Cox. Together they create a tense-filled opposition to Bourne's endeavors. His alter-ego is the utterly talented Karl Urban. Karl Urban as Bourne's alter-ego is interesting. He is what Bourne would be without the drug enhancements and extra special military training. He is as smart as Bourne and as quick-witted. Bourne's decision at the end to not finish Kirill (Urban) off in the car is his acknowledgement that Kirill is as much a professional as Bourne was supposed to be (although I have to admit, I don't really understand "good" guys who have car chases where an unbelievable number of people might get hurt). Karl Urban is also charismatic.
But the third movie has neither a strong protagonist or a strong alter-ego. Joan Allen has been reduced to playing Bourne's second. David Stratharin does a masterly job as a self-contained, nasty character, but Bourne really needs an antagonist who can chew up the scenery, not live inside his part. The two actors who actually could chew up the scenery--Finney and Glenn--are given very minor scenes.("Why?" one asks. "Why? Why? Why?")
And there is no one alter-ego, just a number of possibles.
The movie proves that unless you've got a decent bad guy, you are reduced to a lot of cool action scenes and some good dialog. The good guy can't carry the movie alone, no matter how hard he tries. It isn't that the bad guy and good guy must be in constant communication (a la Bruce Willis and Alan Rickman), just that the bad guy must be out there making life difficult for the hero. Joan Allen never meets Bourne in Supremacy, but her cool intellect is there, searching for him. The hero must matter to the villain. Otherwise, the hero ceases to matter to us.