It doesn't have what made The Bourne Supremacy so outstanding:
The plot is complex enough to be interesting without being absurdly intricate. It is politically relevant without being ham-handed or preachy. It's vaguely plausible, with only a few small holes.
The plot of Ultimatum is trivial - bad guys try to hush up a secret, good guys try to expose it. None of Bourne's antagonists have any agenda other than being against Bourne.
I generally don't like prequels, because the fixed future constrains the story too much. Ultimatum is not a prequel, but by using the throw-away ending of Bourne Supremacy as its central pivot, it voluntarily suffers the disadvantages of a prequel.
There's no real reason why a series of films (or books) have to represent one history without contradictions. If they are really parts of one story, then that's OK, but if not, why not make them alternate versions of the same story? Or different events that could happen to the same characters, but needn't necessarily all have done so. Really long-running series have to accept this - there's no way the events of every Bond film from 1962 to 2008 could have happened to the same person. Terry Pratchett is quite willing to contradict events of one book in another, and handwave it away with reference to History Monks. But it's still not quite admitted outside comedy that a series can reuse characters without being a continuation of the same story.
Back to Ultimatum, it's no mystery why, despite the relative weakness of plot and paucity of character, this film was so well-received. The action scenes - the chases and fights - are much better. They are far more convincing than the ones I didn't like in Ultimatum without being any less spectacular. I would have traded them all in for a plot twist like Danny Zorn's death and a climactic scene like the one in the Moscow apartment.
And it does still have the excellent acting and respect for the viewer's intelligence. Bourne doesn't have to explain that he'd like to keep the girl around, but he can't accept the risk to her after what happened to his previous one - his expression as she cuts her hair is enough for us to know what he's thinking. And if some people miss it, it still adds to the realism that there are things going on that you aren't quite catching. That's what the world is like.

