In Matrix Reloaded, the Architect explains how Zion was part of their plan for the 1% of the population that reject the Matrix, but he doesn't explain WHY the machines created Zion in the first place. Why couldn't they immediately kill the 1% so that they would save the trouble of having to deal with them later on? If the humans are unplugged they are obviously useless, so why keep them around?
Zion wasn't just a refugee camp, it was also an armed base sending soldiers into the Matrix to locate new recruits. Ironically (and unbeknownst to the Zionese rebels), they were actually helping the Machines by using their skill and cunning to locate, remove and then contain potential troublemakers in one place.
Once the numbers in Zion reach a critical level (e.g. where the inhabitants are starting to think about spreading beyond the limits of the city and fomenting genuine unrest within the Matrix) the machines then step in, kill almost everyone and restart the process.
Beyond the purpose mentioned above, the existence of Zion offers four main benefits to the machines;
- It acts as a "safety valve" for the Matrix, collecting malcontents in one place.
- It acts as a supply of humans in the event of the "cataclysmic system crash" described by the Architect.
- It helps the machines to hone their defences against the sort of innovative attacks seen in "Matriculated".
- The One needs to have lived in Zion for several years in order to develop the "profound attachment to the rest of [his] species" that will guide his future actions after the Matrix is rebooted.
The way I understood it was that Zion was something like a pressure valve.
The Architect knew that his equations will always produce a few dissenting humans within the population. These dissenters could destabilize the whole Matrix and bring it crashing down. The equations said that he could never completely get rid of them. So the next best thing to do was to contain them. Give them all a place to call home. So instead of each group of dissenters creating their own pocket of resistance, all of them are now under one umbrella group: Zion. Having all the dissenters in one place means that you can watch them and monitor them. Keep up the illusion that they are completely independent, and they will continue to grow their central city and not venture to split up. And if the humans become too troublesome, well the Machines already know that they are in one place, and it's just a matter of exterminating them all.
I believe that Zion is just another level inside the Matrix. The Machines gave these people the illusion that they are (now) in control of their own body in Zion. But in actuality they are still plugged into the Matrix and are still being harvested of their powers (bioelectricity) so they are not actually useless.
tl;dr: In my view the main purpose of Zion, from the viewpoint expressed prominently by the Architect, is not to collect the rebels but to keep the Matrix functional at all.
At least two initial iterations designed by the Architect were disfunctional. Zion must have been systematically introduced when another program, believed to be the Oracle, provided an unsystematic but functional solution to keep it going.
Since without Zion the whole Matrix fails, its single main purpose is probably to allow the Matrix to remain in working order for extended periods of time.
proof tl;dr: if the rebels were truly use-less or an unorganized threat to the Machines, the Machines would instantly kill them because it is them unplugging the humans from the power-plant, with this robot:
Since the Machines, at least the Architect-"branch" of them, are associated with efficiency and systematicity, the reason they don't kill the awakened humans at this point is most likely because they don't want to.
That rules out all
three now four of Richard's proposed extra main purposes:
If the rebels were useless, they would be killed. Thus:
malcontents in one placeand
supply of humans: no need to wait them gather when you can kill them right off. Without the One there is no anomaly and there is no crash so they wouldn't need an external supply.
hone their defencesand
to have lived in Zion: already dead, they could not attack the Machine City, and they couldn't recruit the One either.
The movie-fact that might include an actual reason for the Machines to allow Zion, is that we've been told the Matrix was needed to be re-designed. Re-based on a different idea supposedly by the Oracle. This idea contains a systemic anomaly - that is supposedly The One. So now the Machines need to let awaken people to live and prosper... because without The One the Matrix just doesn't work.
I think Richard seems to try and convey this by the
beyond the obvious, only it is not obvious at all. Were it obvious the OP wouldn't ask:
WHY the machines created Zion in the first place. Why couldn't they immediately kill the 1%
So isn't it "obvious". I think they might did that in the Architect's two initial iterations. It didn't work. What other purpose do you need?!
I originally had a very long analysis but I decided to remove it. Will share with anyone interested. I tried to make the points in the short versions above. However it also contained passages trying to point out several perceived assumptions in your questions. I re-mention these assumptions:
One assumption is that Zion should be initially machine-built which may be wrong, because the Architect only says that they have destroyed it six times, and that "individuals" will be required to be selected in order to rebuild it.
The other assumption which may be the more flawed is that ther rebels should be deemed "useless" (supposedly by the Machines). They are not becuase if they were then the Machines would kill them when they awake.
There is another remotely connected assumption, that there should be no other forms of intelligence on the planet (supposing there is a planet) but the Machines and the Humans; however, the Machines are mainly associated with Agents, Sentinels, Machine City and the Architect. But the Architect does not exercise control over the Exiles. It is known that they can get things out of the Matrix, so they can live outside it. They behave clearly very distinctively from other machines, the Agents wants to kill them more than the rebels, and they are handled separately in the franchise's supposed canonical continuation The Matrix Online. They can be a third "form"; even more lifeforms are not mentioned although not ruled out either.