I was disappointed too. I thought certain section of the film is just too nagging, some unnecessary (Do we really need the bad French enemies). The 1st one is intelligent and believable, this one is confusing to say the least. Maybe it's just a setup story for the 3rd one.
If Neo is now Superman, and Smith can clone himself forever, what's the point of fighting? And look of Zion city is so uninspiring (compared to the 1st one's human pod scene)....maybe we should let the machine take over.