Problems:
1) It felt like a script was written, and a movie made, and then a few extra scenes were added to tie it in with the Bourne franchise. Of course the whole plot drive was that the agents needed to be taken out, precisely because of Bourne's legacy (due to his going rogue, etc). But other than that, it just felt like a bit of measly attempt to tie this film into the universe of the original trilogy.
2) WHERE DID THAT ENDING COME FROM? We heard about how bad ass this Larax (I think) character was, and we were getting ready for an epic fight scene, yet he dies on the bike and we don't get one. Jeremy and Rachel are on the boat, and suddenly the intro from Extreme Ways comes on, and we were like... What?

But, in all fairness, all the story had was Jeremy trying to get his meds, and escaping from the clutches of those searching from him, once that was achieved. So, without a bit more meat on the story, they couldn't have done a lot more with it.
But, with that being said, there were some absolutely great scenes. The part in the house, where the agents are trying to suicide Rachel, and Jeremy pops out. Absolutely great. That, along with the other short fight scenes that appeared throughout. I did miss an epic clash of the Bourne/Desh vintage, but you can't have it all.
A sequel has been set up, but it has been set up to be focused around the legal battle, involving Landy, Vosen and the CIA. There is nothing else that Aaron Cross could really do within the universe.