Ok, so... Personally, I don't doubt at all that this "colony" might have had something to do with establishing the present "cycle" of human activity.
Reasons-
The Machines have virtually no use for us. I'm sorry but electricity is not a viable option. I have seen some theories floated that we might be harnessed for computing power (see NightTrace in my previous thread) but even this seems doubtful as sufficient cause for this rather elaborate system.
So here is what I theorize (note the use of this word, it is in fact, just a theory). Somehow, humanity has f'd up our world. Wheher it was through the war with the machines or some other means, the planet is largely uninhabitable without elaborate systems to mainain life. Considering the number of people being supported, machine control would be the most efficient and reliable way to maintain life support for hundreds of millions of people.
Furthermore, the Matrix is the kind of world MOST people want to live in. Most humans would not want to live in the cramped caves of Zion, even if we could dig big enough areas to support us all. In fact, I would suggest that if the situation were reversed, and most of humanity lived in cruddy caves and was OFFERED an oppurtunity to live in a simulated world, that the majority would choose to do so.
The problem is that humans would never be able to agree democratically on the form that a simulated world should take. There would be a constant flux of programming changes, people coming and going, there would be virtually no stability to such a system if humans were allowed to choose it and control it.
I believe that at some time in the past, a select group of humans realized this. They established the Matrix with the help of the AI that they had created, as a stable environment for the continuation of human kind. However, it was necessary in the programing to allow for humans desire to have choice. This in turn required the creation of an escape valve, Zion, and also possibly allowed for such anomalies as Neo [[I am assuming for IC purposes that none of us were present for that interview between the Archictect and Neo, and that such information is not widely known.]] Since such anomalies would introduce instability to the simualtion, they in turn needed to be kept in check. The best way to do this was to turn the energies and attentions of the awakened to battling against their apparent "oppressors", and disguise the fact that it was humans who chose to create the Matrix.
To support this are some things we know about the "colony". Halborn claimed to the Oracle to be "hundred's" of years old. Carlyne claims that he is as good as dead, perhaps in a coma. Seeing as he has a ship he can control, he must have been "plugged in" to some kind of onboard computer system, and has been so since before his arrival. He came searching for a "biological interface program", the purpose of which we do not know, but the name is suggestive.
I would suggest that BOTH Halborn and Carlyne exist in a state of physical stasis. I would further speculate that the entire "colony" exists that way. They have kept themselves alive so that they can monitor the Matrix, the situation they have created. I believe Halborn has essentially gone AWOL. He has grown tired of existing in stasis, and sought within the Matrix a program that would allow him to "interface" with a new biological body, thus changing his condition. He is able to overide the programming of the Matrix because he and his people helped create it in the first place. Carlyne came in order to prevent Halborn from achieveing his goal, and to perhaps mitigate his impact on the system. The colony, as such, would wish NOT to be discovered, and our true history revealed, as this might destabilize a system they have maintained for so long. They believe that the Matrix is the best way to keep humanity alive and relatively"happy".
And they may very well be right. We do in fact seem incapable of maintaining stable groups, peace, etc. The Matrix may sipmly be a convenient way to channel these aggressions.
Personally, I am concerned with only one thing: freedom of choice. Those that ACTIVELY seek awakening should be allowed to do so, and as such I will serve Zion to achieve that end. But I cannot support making war against the machines, with the end purpose of destroying the Matrix. To do so would deprive those who choose to stay of their freedom, and I am not a fascist.
In any case, time will tell whether my specualtions have any validity at all. In the meantime, again it seems as though we ought to focus on finding real answers to these questions.