Zion is not the "Real World". No one has been freed. Everything that is happening is exactly what the Matrix wants. The Matrix continues to give humans the illusion of choise. Being able to chose seems to be one of the central needs for humans and that allows them to accept the Matrix program. Now here is some wild speculation about Trinity. I am begining to believe she is a program. Her name means three, we have been introduced to the three parts of the Matrix: the Oracle, the Archetect, and the Core. These three parts protect the Matrix, make sure it continues to function properly. What if Trinity is a mixture of these three parts of the Matrix. Like the anomoly that the Matrix creates (The One) what if her purpose is to help ensure The One makes the choise to continue the Matrix's cycle.