I like the first half because it's full of drama, wisdom (on both the "good" and the "bad" sides), and emotions gradually grow, as well as audience' awareness of what is happening. Forget about Jason Bourne, there are much more going on there, compared to which, an amnesic agent who is fighting to regain his identity looks just trivial.
Aaron Cross actually got "profit" from the Outcome program -- his less-than-average intelligence got improved. And he doesn't want to lose it, which makes him not look so "moral" -- he stays in the program just to stay away from a even worse life, while his recruiter, Byer, and even Dr. Shearing, believe(d) that they are serving their country, at least.
I feel that Cross started some casually romantic feeling towards Doc during the repeated visits for examinations. I mean, you don't really count the times you meet a certain doctor in a few years, unless you have some special feeling for him/her. And that near "harassing" lines inside the examination room...
While Doc started to look at No.5 in a different way when he was focusing on preparing a fake passport for her. Maybe that was the first time that she saw one of her "participants" really working in the field. There's the saying that "Man who is seriously working is the sexiest" (or some line like that), absolutely true.
The script is really "wide-open", in the sense that now anyone can add in another new program at any time. So there can be endless hunting, endless new agents/opponents, therefore endless sequels, if fans buy it. James Bond must get envious, cuz he cannot even kill a bad guy too fast sometimes but has to keep that for a future sequel. My only concerns are, first, now they've used up the idea of high-speed chasing and chaotic parkour in a crowded city, what other fresh things they can come up with next time? And second, since Aaron Cross has got permanently "infected", he needs the pills NO MORE, so the story actually needs the Doc NO MORE? hmmm that's a dangerous sign for a hero's lady in such a franchise...
P.S. An interesting finding: Outcome had 6 remaining agents when it started to be burned down to ground. We've known that 4 were killed (1 in Pakistan, 1 in Seoul which I believe is the one undercovered into N-Korea intelligence network, the lonely ranger who got "demoted" for falling love, and No.6 who is the black guy), No.5 a.k.a Aaron Cross managed to escape, so who and where is the last one? A thread for sequel? Hope they didn't miscount...