The Bourne character had to be a little more resourceful than bond ever did from what I've seen. Not only did bond have the support and inventions of MI6 but most of bond's objectives were planed out.
Bourne had not only assassins but the CIA after him while he had amnesia and was able to plan and execute his own objectives.
As another poster pointed out however
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Bond would win because Bond is proactive in finding and destroying his enemies, whilst Bourne is reactive, finding and destroying those that try to hurt him first, who are inept, luckily for Bourne. If Bond and Bourne were to be opposing, Bourne would not even know it until after Bond took him out, and Bond is not inept like those others.
So it would depend on the situation.
If Bond was sent to kill Bourne I believe Bourne would have less of a chance because bond rarely makes mistakes, especially if Bourne didn't know he was coming.
If Bourne was sent to kill bond (who would probably be busy with some blonde girl) I think he might have more of a chance.
If you put both of them in an empty locked room I think Bourne would win because bond rarely kills his enemies with his bare hands, he usually uses some weapon or trick.
I probably thought about that way more than I should have.