Sorry, Neo: I'm Rooting for the Machines
The two Matrix films to date (though particularly the first) exhibit surprising complexity, capture a certain zeitgeist of the internet generation, and largely deserve the critical acclaim they've received.
However, I submit there is an additional layer of moral complexity to these films which has largely gone unnoticed: which side you should root for. Just as at the beginning of The Matrix we assumed that the 1990's environment was "real" just because we're seeing it, so we assume that within this story the humans should win their war against the machines just because we're human. Looking at these two movies more carefully reveals many reasons why the machines may have a better moral and ethical case for their current status quo, and adds a layer of moral illusion to the these films' theme of perceptual illusion.
Two things I should get out of the way first...
I'd like to keep the next section streamlined so let's get two things out of the way first:
The machines in The Matrix are intelligent, sentient, self-aware, and alive. I'm mentioning this because if you don't buy that they're alive then you're not going to buy that they should be regarded any differently than rocks. However, I don't think this should be a big point of debate: even we referred to them as "Artificial Intelligence" at the time we created them (which was obviously long before they developed to the point they're at in The Matrix), they obviously pass the Turing Test since Neo talked to the Oracle at length without realizing she wasn't human, they reason, they have goals which can change over time, they can disagree with authority and rebel (as Agent Smith did in the first movie and as the Oracle indicated many others have), they want to protect their own existence and will accordingly in creative ways, they clearly have emotions (to judge both by Agent Smith's disgust at how we smell as well as his fear at being "corrupted" by our world), they appear to have a moral sense (to judge by Agent Smith's judging us for how we mistreated our environment), and to judge by what the Architect said about the Oracle in the second film they can even exhibit a quasi-mystical facility of intuition. In short I can find no basis within The Matrix for believing that the machines are any less alive than we are.
If the machines in the Matrix aren't more intelligent now than we are, they will be soon. Freed humans in the world of the Matrix have the same physical brains that we do now, as can be judged by the fact that using these same brains the 1990's simulation of society looks the same to us, and people behave more or less the same, as we observe them as behaving now. This is what one would expect given that Darwinian evolution basically no longer applies to humanity, and hence no longer drives improvements in our physical forms. However, the machines ARE evolving, and can drive their own evolutions through "upgrades" (as Neo noted in the second movie). In brief, if they aren't more intelligent and sophisticated than us now, they will be shortly. To judge by how easily we can communicate with them they seem capable of thinking the same kinds of thoughts that we do, but perhaps with upgrades they would be able to arrive at understandings and appreciations of the natural world that would far exceed the limitations of our physical minds (i.e. if nothing else their intuition wouldn't be limited to three physical dimensions and non-relativistic non-quantum scales).
Anyway, moving on...
Reasons to root for the machines
Our environment is permanently destroyed while theirs is not. The sky is scorched. As far as I could tell from watching these two films basically every non-human form of animal life is extinct, all of the world's plant life and forests is dead, and the surface of the Earth is cold and uninhabitable. They didn't say much about the oceans but I find it hard to believe that the chain of life which begins with the sun feeding plankton could have survived. In short the Earth is barren and ugly, we can't get back the life we extinguished, and apparently we can't even restore the sky because if it could have been done the machines would have done it (interestingly enough the machines needed it but we apparently felt we could do without it...). The Earth is now a hellhole from the perspective of humanity, but the machines probably don't mind as they're probably not hardwired to find beauty in the natural environment in the same way we are, and so they may not perceive the earth as ugly.
We have nothing to do once we win the war other than go back into virtual reality. If there's one thing humans love, and which makes them feel alive, it's engaging in a noble battle for our survival. I'm sure this is invigorating for the inhabitants of Zion, and that their war against the machines keeps them from falling into despair over the state of their planet as they otherwise might (i.e. just as our war against Iraq kept our citizens from falling into despair over our own economic and leadership crises). However, what exactly happens once we win the war with the machines? We're faced with no enemy and a ruined earth. Again, we can't get the sky and hence the biosphere back because if we could have then the machines would have. What, exactly are we going to do other than turn back to virtual worlds for escape, once we no longer have to live in fear of sentinels drilling down to Zion and wiping us out? And if we turn back to virtual worlds, then how exactly is that different from continuing to live in The Matrix? Keep in mind that the machines originally tried to give us a virtual paradise but we rejected it, and that the matrix went through several iterations before arriving at what was apparently the pinnacle of our civilization in the first movie. As such, given that once winning the war we would probably retreat to virtual life anyway, we couldn't even create a virtual world for ourselves which we'd enjoy more than the current one we're unknowingly stuck in.
We started the original war with the machines without a shred of moral justification. This was revealed in the Animatrix backstory and was hinted at during the first movie (We remember that we scorched the sky but somehow forgot who started the war? Please, I'd be willing to bet that if THEY started the war we'd have remembered...). In any case, the back story from Animatrix is that long before The Matrix we created artificial intelligence and promptly deployed these LIVING, SENTIENT, and INTELLIGENT artificial life forms as slaves to do all of our menial labor. To make matters worse, our citizens regularly gathered into mobs to beat and kill them for sport, and our courts ruled that they had no rights nor legal recourse no matter how badly they were treated. Out of self-defense the machines formed a nation of their own (called "01" as I recall). 01 proved to be a productive nation that excelled at creating quality machines and consumer goods, and as such the economic power of their nation grew. This led to tension with the human world and conflict. The machines petitioned the UN for membership several times, seeking peaceful co-existence, and were rejected each time. Finally, humanity as a species decided through the UN to attempt to wipe artificial life off the face of the earth, and so launched an unprovoked series of nuclear strikes against 01. The machines survived but realized that their survival was threatened, and so defended themselves. All I can say is this: if I were an impartial outside observer watching all this happen, and was asked to pass judgment on who was right and who was wrong in this conflict, humanity would lose: we engaged in a series of unprovoked moral horrors, rejecting every chance for peaceful co-existence, and finally tried to wipe another intelligent life form off the face of the earth. Since losing the war, the fact that we get to live on (in a way and at least for a while) is a bonus that our species in no way deserved.
The chances of survival and pain-free existence for BOTH species is higher if the machines win the war than if the humans win the war. We've already decided that we want to exterminate all artificial, sentient life, and would do so given the opportunity. To wit, we established that in originally starting the war with the machines by thoroughly nuking their homeland ("01") just because they were doing well economically. We established our sense of justice even earlier by beating and killing the machines for sport once we'd enslaved them. Now we have the same minds and the same instincts, yet we're at war with them. Will we really be any more compassionate towards them this time around if we WIN this war? Of course not, we'll just wipe them out. Let's contrast this to the machines: even after winning the original war and losing many of their numbers to our attacks, the first matrix they created for us was a PARADISE. Of course they probably believed that this was in their best interests, but that's not the point: the point is that they didn't go out of their way to be vindictive and create a hell for us, as to judge by how human victors have historically treated their captives after and during a war we probably would have.
We'd probably just create artificial life again and suffer all of this again, if we win the war, hence creating the same damned situation all over again. We want our lives to be convenient. We want other people to do work for us. We want to be entertained. We're not going to just forget how to create artificial intelligence, and after winning the war we'd have the same brains and same set of underlying motivations that we did when originally creating the AI/slave race. I'm sure that the taboo against creating more artificial intelligence would last for a few generations, or perhaps for a few hundred years, before underground experiments start happening and a black market in AI gear starts appearing. We rationalize what is easy, as we always do, as the memory of the war fades. And eventually we're back in the same damned situations except maybe THIS time the robots will be based on something other than solar power (which makes sense given that we won't have solar power to base the new ones on) and hence there won't even be a point in their keeping our species around for use as batteries.
Machines are better geared to survive than we are. Humans have certain legacies of their evolution which are proving difficult for us to overcome. In particular the charge which Agent Smith leveled at our species in the first movie (that we don't live in balance with our environment and left to ourselves will consume every resource without regard to the future) went unanswered in The Matrix probably because there IS no answer: it's TRUE. It is the nature of our short lives that we don't think of the future, and we're given to behavior which may have helped us back when we were evolving but which threatens us now. But by contrast, machine life isn't dependent on cells which age, and there is no reason why these sentient, self-aware artificial life forms won't just life forever. For that reason, if nothing else, I believe the machines would take care of the earth's non-renewable resources in a more sustainable and responsible manner than humans would. And eventually this WILL matter, because (if nothing else) when our sun expires whatever intelligent life is left on Earth will need to move elsewhere, and for that reason there will need to be enough mineral and chemical resources left to accomplish large-scale space travel. Up to that point there are many types of problems which machines could survive which we could not, and ultimately I think it's the survival of intelligent life that matters more than its form.
Aren't machines how we'll end up anyway? What human wouldn't want to live forever and feel healthy and young every day of their lives, even after thousands of years? Our current bodies can't do this, but machines can. We'll want to move in that direction eventually. So, if the reason we think humans rather than machines should win the war in The Matrix is based on the fact that our species should inherently be preserved, to me that's a shaky proposition because at some point we won't be human any more by our own choice.
Maybe we need to learn to let go and trust that this is another form of the same upward complexity drive that produced us. I've never had children but it's interesting to go back to how Morpheus put it in the first movie: that we "gave birth" to AI. Interesting. Since it wouldn't be that long before the machines are more sophisticated and intelligent than we are (if that isn't the case already in the world of The Matrix), maybe if they won the current war with the humans it would simply one generation taking its place after another.
It's hard enough maintain perspective when your family or friends are involved in a conflict, much less when your entire species is involved in a conflict. Yet, that is the nature of the fictional world of The Matrix. This movie and its sequel explicitly addressed the implications of our beliefs about the world being tricked because we want to believe what we see, but was much more subtle on the implications of our moral sense being tricked because we want to believe that our own species is automatically right.
I would like to suggest that the information presented in the two Matrix films so far do not suggest we're in the right, and I hope that the next Matrix film addresses this question head on.