i say you are really making this way to compicated.
You can not keep assuming that the programs are lying to neo. In fact that isn't even possible since a program can't lie. That is a human trait. Programs do what they are programed to do. The arch fucntion is to get the code from the one and re-insert it. He is not there to play games with a human.
And how can you say that there is no free choice. You miss the entire theme of the whole triliogy when you say that. Since movie one it has been about choice. Neo chooses to save morph, to fight agent Smith, to believe he's the one.
In the second movie Trinity chooses to enter the matrix even after neo warned her. Persophene chose to help them even after her husband refused. To overlook choice makes it seem like you watched the movies with your eyes closed and your ears covered. It is totally stupid.
But to be fair you have your opinion and may turn out in the end to be right but i say that is highly unlikely and i desperately hope our two brothers are more clever than that.