The Analyst is the creator of the Matrix version 8.0. This new Matrix model was not based on choice, which in turn allowed for a purge to take place, deleting all purposeless programs and exiles, including the Oracle. For more on this, see Matrix System: Revision History.
While the Analyst certainly understands humans magnitudes better than the Architect did, I do not believe the Analyst understands humans better than the Oracle, contrary to what many believe. I also believe the Oracle was able to evade the purge by going into hiding. For more on all of this, see Oracle: Baking Cookies ("Trinity in M4"). In fact, the Oracle's powerful vision is precisely one of the reasons machine society would have wanted her to be purged. For more on this, see Oracle: Choice ("Oracle the Terrorist").
An additional reason why the Oracle would have been purged at the beginning of the Analyst's Matrix is to ensure that no other programs exceed his understanding of humans, as a way for him to survive, should things go bad. Had the Oracle been allowed to survive under the Analyst's Matrix, the Analyst probably would have been purged at the end of M4, with the Oracle taking his place, being kept around because "I know the system, I know human beings, I know you."
When bluepills escape the Oracle's Matrix, they are given a fair amount of freedom to do so. The Analyst's Matrix is another story. When Neo is ready to step off the building and try to fly again, even though it's very late at night, his coworker Jude calls him. This couldn't have been a coincidence; the Analyst must have an automatic detection mechanism in place so that he knows that Neo is doing at all times.
The best example of this is what we see immediately after Neo takes the red pill:
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Seq: Captain. I’m tracking a whole lot of weird.
Bugs: What? Seq: It’s some kind of graft. Analyst: Thomas? Neo: Oh, God. |
Of all the weird, random things that Neo could experience when he touches the mirror, why would the mirror just happen to create a portal into the Analyst's living room? There is no way this is coincidence either. The Analyst monitors his Anomaleum bluepills very closely and does everything he can to deny them choice, even when it comes in the form of a conscious, deliberate rejection of the Matrix itself.
It also seems odd to me that, as far as I could tell, literally every single passenger on the Japanese monorail was a bot for the Analyst. At first, this made me wonder if Neo and Trinity were in their very own Matrix, separate from all other humans. But it could also be another aspect of the Analyst's control. The Mnemosyne crew might have used that portal before, so the Analyst made sure plenty of bots were planted in that car of the train in case it was used again. The far less satisfying answer is that it could be that an element of scriptwriting convenience: there needed to be a cool fight scene on the train with lots of enemies, so with a swish and flick of the scriptwriting wand, 100% of the people in that car of the train were bots, and 0% of them were bluepills.
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Analyst: Fail Safe Back to Introduction |
 Architect: Equation |
 Analyst: Fail-Safe |