Whenever possible, the Overide (if necessary) in respect to a Christian view of free will and freedom will be reinforced. This view holds that free will is sacred and that freedom is not dictated by circumstances but by self. Even in the face of Fate and Determinism, for the individual, choices remain and are important.
Evidence
1. Cage to chrysalis speech by The One at the end of the shooting script.
2. Spoon Boy's comments about the truth and what actually bends.
3. Neo constantly presented with choices.
4. Christian allegory.
Objections
Why this philosophical point while ignoring so many others? Well, because this one happens to integrate itself nicely into several of the theories discussed above and helps to illustrate a principle valuable to that discussion. If another philosophical point was as useful here, we'd use it.