1 The goals are different. There are three forces in this film, one is Byrne (to live a stable life and to retrieve his lost memories) and the other is a killer (to kill at all costs) Killing Bourne and framed Bourne) The third is the CIA (because the killer framed Bourne, which made Bourne the most wanted criminal in the CIA)
2 The action is different. Bourne has always been running away in the first half, only in the back because His relatives were killed, so he started to fight back. However, other forces have always been real guns and live ammunition.
All in all, I think the best thing about this movie is that it portrays a wanted man who kills people often (although all killers are killers) as the incarnation of justice.
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