Well, like I said, there was some sort of emotion in the first. In reloaded, everyone was "cool".
However, what you said brings me to something I've been wondering about since the first moive: Is the Matrix really evil?
Think about it, what has the Matrix done that's really evil? Sure, it uses people as batteries, but it seems more symbiotic than parasitic. After all, the Matrix even tried to create a perfect world for people to inhabit.
Okay, an agent may inhabit a person, but who's to say that this destroys the human?
Perhaps we could look at the movies like this:
The Archietect is God. He created the world and controls it and has a plan for humanity. He tried to make the world perfect. But humanity by its very nature can't exist in such a state, so he made it as perfect as the human mind can comprehend.
Morpheus doesn't like the plan. He believes that he knows how to govern his life better than God, so he leads an uprising.
However, Morpheus has forgetten that God is omnipotent and, as a result, his "revolt" is all part of the divine plan.
That would make Morpheus Lucifer.
And, when you think about it, what kind of world does Morpheus offer humanity? A blasted out wasteland. Can anything grow there? What about other animals? Unless there's livestock in the matrix they can free, how does he plan to feed a couple million people? How many people would thank Morpheus for what he's done?
Most people would look upon the world Morpheus offers as Hell.
The movie already has religious undertones (the names of the characters being the most obvious). I doubt that the producers would go so far as to make the heroes the villains by the end of the trilogy, but it would be interesting to have humanity reject Neo and Morpheus and prefer to stay in the Matrix.