These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
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.
Ensemble Darkhorse: Arguably, 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.
Gary Stu: As this very page probably suggests, Ken himself arguably edges into this, particularly later in the story (though it should be noted this page does not include tropes already existing in canon).