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If you see Ultimatum, much of his struggle to deal with who he was, who he was turned into, and why, and who he is now, is what the movie is about.
As opposed to "Identity" and "Supremacy" -- which concentrated on Jason Bourne struggling to deal with who he was, who he's turned into and why, and who he is now. :)
At least James Bond knows who he is and who and what he's fighting for; Jason Bourne, fittingly, will likely never really know -- taking deniability to the next level!
The moral agency of Bourne's actions is another casualty of the forces that created him -- while Bond is comfortable doing dirty deeds for Queen and Country, Bourne's a mostly blank slate.
Bourne benefits from the knowledge he's gained on an operational level, but where Bond is suave, outwardly cultured and sophisticated -- an agent free to make choices and decisions, Bourne is kind of a killing machine on autopilot -- just put him in a situation and he reacts instinctively, or else he responds tactically to the needs of the moment. This creates still more deniability for him as a character -- he can't help himself, he's just been trained to be that way; he's Pavlov's Dog of Secret War.