When Neo meets the Architect in the "television room," not only do we see possible choices that Neo is making, but we also see archived footage of past Ones. Many (or all) of the past Ones have the same RSI as Neo, the sixth One. Why would all of these past Ones have the same RSI as Neo if they are all different individuals?
Nature: It wouldn't make sense for machines to use different DNA each time the One is born. We must assume the One is designed to be as perfect as humanly possible (pun intended) so that the chance of his fulfilling his designed purpose is mathematically maximized. In fact, the Architect refers to this when he speaks of the "contingent affirmation" in the design of the one. Even Neo's propensity for love has strong genetic basis. The Architect simply couldn't talk about the "design" of the One if DNA weren't a huge part of that design.
Nurture from machines: It’s likely that the Matrix system guides Neo to have nearly the same experiences with every iteration of the Matrix to ensure The One won’t give the Architect any surprises or complications whenever it’s time for the big choice. The Architect noticed a lot of differences in this sixth Neo from previous Neos, and if the system is trying to ensure that Neo is as similar as possible each time he arrives, but one time he arrives quite different, then the Architect would know that the Oracle is responsible for such drastic changes to The One via her “baked noodle” manipulations as well as cookie code manipulations. That is why the Architect said to the Oracle in the end, "You play a dangerous game."
Nurturing from rebels: Neo’s RSI would likely be identical each iteration of the Matrix when the training he receives is probably similar or identical each time. When he first enters Matrix simulations, his RSI is just a regular guy in a black outfit with a normal haircut. But after he gets his intense training in martial arts, guns, technology, and who knows what else, this rebel training would surely dominate his RSI. Presumably it equals the amount of training we could only receive after two or more lifetimes of mastery in multiple disciplines, so rebel training is no small thing to consider when it comes to RSI.
Notice that Morpheus and Trinity (who received the same training) have similar RSIs to Neo, most notably black leather coats and sunglasses. We have slight variations (i.e., different shaped sunglasses and different leather coat styles), but still basically the same thing. Niobe would be another example, only with dark purple leather. These are all rebels who no longer fit into normal society, all of whom probably had drastically different RSIs before having their minds freed. The only rebel who has a drastically different RSI is Switch, who wears white, perhaps because of being bisexual or transexual.
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