I was quite disappointed in the movie. It isn't bad and it sets up what should be a few good movies down the road, but was just disappointing. Here are some the reasons why:
1) It's all about the drugs
After Aaron Cross nearly gets killed in the beginning of the movie, you think he might want to get revenge on his handlers? Nope. What does he want? Drugs. I couldn't help but think during the the movie that badass Aaron Cross is just a junkie, "Where are the chems?", "Do you have any chems here?", "How can I get more chems?".
Similar to the "midichlorians" in Star Wars, the drugs also removed some of the allure of the Treadstone/Blackbriar programs. Rather than brainwashing and training the agents, are they just druggies?
2) Aren't spys supposed to be secretive
During the end chase, the Larx-3 agent punches a bunch of citizens and attacks cops. He does it multiple times.
I thought these guys were supposed to be spys and hide and be "ghosts" (I think they were referred to this in the first movie). Now this isn't to say that Jason Bourne didn't get the attention of the police, but he did seem to make a number of attempts to not get engaged. In the Bourne Ultimatum, the asset kills Simon Ross via sniper rifle. Larx-3 could have done the same thing too, but he decides he wants to chase them on foot.
3) Where's the super spy fight
Every Bourne movie to date had a cool fight between Treadstone/Blackbriar agents. No fight in this movie. In fact, Aaron Cross had a little trouble against the normal agents he fought in the house. I was just waiting for him to fight Larx-3 at the end of the movie. Only to find Larx-3 was taken out by wiping out on his bike.