Many who watched M3 felt the trilogy was pointless since Neo did not destroy the Matrix or set all humans free. But in closer examination of what Neo changed, the meaning of M3 becomes far more significant (and the ending becomes more emotionally powerful).
First, Zion will be allowed to survive since Neo ends the war. That means 250,000 humans will not be slaughtered, which also means that if the peace agreement is ever breached, it will be more difficult for the machines to destroy Zion again. But believe it or not, this fact is almost negligible compared to the larger mission Neo accomplished on behalf of the human race:
Oracle: What about the others?
Architect: What others?
Oracle: The ones that want out.
Architect: Obviously, they will be freed.
Oracle: I have your word?
Architect: What do you think I am? Human?
From this conversation between the Architect and Oracle at the end of M3, we learn that all humans who reject the Matrix will be allowed to go free and join Zion, rather than having to deal with "splinters in their minds" for their entire lives (see Matrix System: Natural Redpills for support of the idea that people who previously rejected the Matrix never went free unless they swallowed a red pill from a hacker).
Neo requests that peace be allowed if he succeeds at destroying Smith, and the machines honor the request in its full sense. Not only do the machines cease attacks, they will also allow those who reject the Matrix to go free instead of keeping them enslaved. Thus, the Architect’s rhetorical question “What do you think we are? Human?” refers to the fact that the word of machines can be trusted while the word of humans cannot. When the machines say “peace”, they mean it. But just how many people are we talking about? Hold on to your britches.
Remember that Agent Smith said in M1, "...the Matrix was redesigned to this, the peak of your civilization." We know people reject the Matrix at the rate of 1% from the speech the Architect gave in M2 (it was actually a little over 1%, but we'll call it 1% for the sake of being conservative). In order to avoid confusion, let's only look at the new generations coming about within the Matrix starting at the end of M3.
This scenario of 12,500 people choosing to escape the Matrix represents only one year of births, and this scenario is happening over and over again with every new year. So, under this scenario, approximately 12,500 people per year escape the Matrix, which is about 34 people every day!
The real world is going to experience a normal growth rate from its own reproduction, on top of a completely unnaturally high growth rate that will always be based on one percent of the birth rate inside of the Matrix. This represents a more serious real-world threat to the machines if peace is ever broken. It also seems that the humans are going to have another big problem in the real world from this point on: how do they accomodate a city growth rate of 12,500 people per year (not including Zion's own birth rate)?
Granted, this whole argument rests upon the assumption that the population of Matrix-grown humans is equal to the population of humans at the peak of human civilization. Surely, most humans died in the war against machines before the Matrix was created, so this assumption might seem a bit silly at first, since Machines can easily design a Matrix simulation with any number of humans and construct a "human history" timeline to support whatever population actually exists. But remember that Machines can grow as many humans as they want, and in fact the more humans they grow, the more electrical and computing power they get. There's no reason to believe that machines wouldn't be able to produce crops of billions of humans in a fairly short amount of time.
All that aside, regardless of actual numbers of the situation, the concept of true human freedom is core. Instead of being given a choice to be dumped down a toilet drain and eventually slaughtered by sentinels that dig down to Zion, humans will now probably wake up in a more pleasant manner and be escorted by machines themselves to a city without the threat of attack.
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