Wachowski bros and religion.

My praise to the Bros for taking comic book movie making to a greater level of eye candy. I’ll certainly be paying my $7.50 to see Revolutions.
But I’m a review whore and have peaked at some of the spoilers, and it seems that the Bros promising risk-taking philosophical questions from Matrix 1 end in Matrix 3 with a Jerry Bruckheimer style.
Now, I haven’t seen the movie yet, but the question I have is: Why do such brave risk takers end up folding in the end?
Why do people who dare to challenge religion never follow through with it?
Or even more specifically, why do people who dare to challenge fundamentalist types who interpret metaphors as literal truths never tell them in the end that they are just plain wrong?

As much as I am a review whore, the Bros seem to be religious whores who skimmed the surface of world religions and made a great sci-fi yarn, but why didn’t they make it even better by plunging deeper?
I guess we’ll have to wait for the Matrix4 video game.