My biggest problem was the dumming down of the non speaking agencies. So Dr Ryan is the great financial analyst, okay but once they figure out the plot the professional man hunters can do nothing without him thinking of the target first. The NYPD and the FBI who actually practice counter terror depends upon him a CIA money tracker to think of checking under the building for a bomb. Because he just was eye to eye with the biological parent of a sleeper suicide bomber he is able to get in the kids mind? And just how are Russian foster parent sleeper agents able to raise a kid in America and convince him to be a suicide bomber for mother Russia, that is the story I want to see.
I prefer the way Ford and Dafoe played it in Clear and Present Danger. In that case even though cut off from everybody it wasn't a case of I am Ryan and can think of everything myself. In the end having the world travelling spy come back to New York in the last seconds to take charge was better played in The Peacemaker with George Clooney and as that was before 9/11 you had an excuse for the cops not willing to take the shot or waiting for the CIA to save them.