Initializing the Matrix- that is, starting it up in the beginning- was a unique and tedious event unlikely to be easily replicated. People woke up inside with no memories but had skills and a context from which to begin their lives. The Agents buried the public memory of the Awakening through aggressive tactics until any trace of that memory disappeared.

Argument

This is our view of how the Matrix was initialized (which will most likely be torn apart by the SRpt2, heh, but seems to be logical): Through brute and tedious force, a million (I dunno, a small- relatively- number of people) are placed in their homes, jobs, etc. and they awaken. These are "virgin" minds with no previous memories to delete or alter. Using the Skill Download technology, these people awake with skills and abilities (NOT memories or beliefs which begins to create the same Agent Neo plot hole). Then the Matrix is turned on.

Aside: What we mean by "brute force" is that a fictional life is created for a person (most likely extrapolated from a real person's life found in historical archives). Tax forms, church membership, a home and a job, etc. Then people are placed into the home or job. When the Matrix intializes, Mom finds herself standing up preparing breakfast and pregnant. Dad is reading the paper. Even though they remember nothing, they assume they are a married couple and piece together their lives from the evidence they have.

In the right context with the right skills, the humans will put together their own conclusions of who they are despite their amnesia. Slowly, but surely, society will begin to move forward because it must. Now in normal human society, there would be memory of the Awakening... but how does memory exist today? In books, print, electronically... basically media. Anytime a book about it would be published, it would be shut down by the Agents. Articles would be stopped. Every means of publically sustaining that memory would be attacked by the Agents. At the same time they would provide the humans with other media and things to worry about. An earthquake hits and that's all the news-cycle can talk about (it helps explain missing data too).

Gradually the generation with amnesia dies off. Personal word of mouth knowledge, diaries, etc. of the event still exist but what real impact would they have? Any attempt at disemenating that information on a large scale would be stopped by the Agents (who would no doubt kill the source too). Some level of oral tradition might remain, but why would you believe grandpa that everyone woke up one day with no memories? You have memories and you've never read anything about such an event in school... oh, silly grandpa! Any serious oral tradition (one that tries to spread) will be detected and killed... and even if not, lose more and more credibility. Their secrecy protects them from the Agents, but makes their story less and less feasible.

All the while society is growing larger, more complex, etc. The Agents spur development of more city scape on, always making the humans think it's their idea. History books can now write themselves and the media be left alone (more or less, except to stop technological or philosophical development). With a complex society of strangers, the machines can now begin to insert more and more people into the gaps. People with amnesia waking up in apartments and a fleshed out life and skill set, with society as whole moving around them, they just accept it and move on.

Any attempt to record or report on the relatively high occurence of amnesia is killed off... it's subtle, so few would notice anyways, but if you imagine a doctor beginning a paper to be published (he sends it to the editor to check it out), then suddenly finds his practice sued, his life destroyed, and his credibility shot.... etc. etc. etc.

Our theory is that the Matrix is at critical mass at this point. With no insertions necessary. To reload, you'd have to go through that whole mess all over again starting from the beginning with virgin minds... test trials could be run with people who have existing memories, but they'd probably always try to wake up, recalling their past lives. Entire crops would be lost.