That Bourne Picture

I didn't like The Bourne Ultimatum, other than a fight scene between the Matt Damon character and some assassin who just isn't quite good enough at his job to stay alive. Stephen Hunter, my favorite film critic, didn't like it either. He explains the plot like this:

Jason Bourne, who two movies ago awoke with no memory while floating face-down in the sea but with a great number of alarming, unexplained skills (he can start any motor vehicle with his fingernails and flip any 10th-dan black belt into the balcony), is closing in on the puppet masters who vacuumed his brain and turned him into an assassin automaton. (Clearly, I have failed in my attempt to convince the American people that "amnesiac superagents" should be banned from the movies.)

In any event, after the movie's dim opening (to connect it to the last one, which ended in a car chase in Moscow), Bourne is headed to England to link up with a British reporter who has knowledge of the black op that programmed Jason, while the agency is politicized (Allen is the liberal exec, Strathairn the conservative) by the crisis and tries to either kill him (the con position) or bring him in (the lib).

One of my quarrels with the entire Bourne storyline is that a paranoid picture is painted of a CIA which is ruthless and all-knowing, yet simultaneously totally incompetent, unable to achieve the tiniest of goals. Why should I the audience member fear the film's antagonist, which (1) can't even prevent unauthorized persons from entering its headquarters (and 2) whose employees handle classified material before wide-open windows (and 3) is so sloppy in its super-malevolent assassinations of, among others, newspaper reporters who have just written damaging stories about it that those assassinations can be easily inferred as to have been carried out by it?