I think the Brother's might be a step ahead of people with this.. (I'm going on the limb) by saying this..

Reloaded is not a complete product.. The introduction of Zion, the dialoge at the restrurant, the long fight scene with Smith, all have purpose.. and we will find them out in the final of the trilogy..

I think the answers of will, choice, control, and power will be given at the conclusion of the film..

just my take..