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The only issue I have is how she became the consciousness of the IS. i don't know why she became that way or why shenchose that path in your route.
Originally it is made clear Sae did not want to become an equalizer. But she was beaten by the terrorist who was already in 2nd shift as she was. At that point she was already dying. In a last ditch effort she activated her IS and forced the equalizer protocols to breakdown her body into data and reconstruct herself in her prime form. Ofcourse this meant she would be listed as an equalizer rather than a pilot. However this retranscription of her database granted her 5 minutes of practical immortality. In those 5 minutes she was no longer contrained by the limits of human flesh in terms of mental processing, physical strength and reaction as well as regeneration more accurately described as repeated reconstruction. When the 5 minutes finished, Sae is completely registered as an equalizer and loses all rights as pilot. She is broken back down into data and sleeps in the IS core.
So maybe make the way she turned into the core a bit more poignant by giving a reason why it was necessary.
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