Big Lipped Alligator Moment: Ken's encounter with the scientist responsible for making him a Coordinator, DoctorHeinrichMetzinger. Metzinger turned up once, long enough to be sliced in half, and was scarcely mentioned again. In actual fact, this was part of a poorly-handled attempt by the author at a Metal Gear SolidShout-Out, most of which was ultimately mostly abandoned. The author has vague plans of turning the botched plot into the basis for a further installment of the Falconverse, but for the moment, this sequence remains orphaned and seemingly inexplicable.
Common Knowledge: Thanks to the author naming the Neutron Stampede platform as the Marie Curienote the scientist who discovered Radium & died of radiation poisoning, almost everyone now believes that to be the name of the ship, despite being officially unnamed.
Ensemble Darkhorse: This fic spawned a trend of fanfics with a ZAFT-centric POV, as well as a greater awareness of SEED-MSV character Shiho Hahnenfuss.
Also, OC KarenWillet seems to have reached this status.