In the original drafts, the Bourne/Nicki romance connection was made absolutely clear in that they both were an item before Bourne went amnesiac on her.

Ultimately, Greengrass was wise to dump it. Its still subtly clear in their scenes and dialogue ("You don't remember, do you?") so Greengrass can make THE BOURNE ULTIMATUM the best of the trilogy without story-junk getting in the way of the narrative. Plus, the audience at my screening LOVED Julia Stiles' smile at the end.

As for AngelaMarie's contention, I would argue this.

If Marie had lived, Bourne wouldn't have gone searching for his past. He says so in IDENTITY. But since she got skull-capped, he gets his revenge on the killer, but the pain stays. He apologizes to the poor girl whose parents he knocked off, but the pain stays.

So its part of this whole chain of events for him to get "revenge" by going home and knocking down the walls of the CIA.

Or, he's curious. Perhaps Bourne always knew that he willingly was engineered into an ass-kicking machine, but how does he know for sure? Its like those adopted kids who just can't put away trying to know who their real parents were.

But as soon as Bourne gets hooked up with the journalist, his war intensifies.

Its no longer the CIA mistakenly thinking he's gone rogue, or the CIA mistakenly thinking he killed agents in Berlin, its the inner-cabal of the CIA effectively going rogue themselves, killing anyone that gets in their way(even their own agents) and Bourne just fucks them up the ass.