Interesting story. Of course its technical aspect will not make it enjoyable to all readers like it is for this crazy computer engineer here. You make a consistent explanation for the abhoring events of Rika creation, based on Nei, and explains in a creative way why it took so long for Seed to create Rika. It is consistent with the PS timeline (the true explanation, though, is that Naka, Kodama and the others couldn't get over Nei's death and acted like 8-years-old, coming with an absurd explanation to throw a Nei's facsimile in PSIV and give her a silly Final Fantasyesque happy ending - rant over

). Anyway, great job, though not for general audiences.