There's probably tons of reasons some major characters didn't find their ways in (in part from the slightly lesser roles they played), but I am, perhaps foolishly, surprised Dilan and Aeleus, particularly Dilan, get sidelined so hard. If the KH3 chess set is any indication, it seems Nomura originally had plans for Xaldin to be one of the 13 Darknesses, right? I guess he had a hard left turn on that idea and hasn't come back.....though it does make me wonder why we still have his chess piece, both in the physical set and in the cutscenes.
And as many above have said, I'm just overall bewildered by Ienzo in the Org section. Like, sure, he was part of the old Org, and I guess traitors Demyx and Vexen are there as well, but...he definitely sticks out like a sore thumb, and sorta perks up some long-running suspicion I've had for Ienzo (or, Nomura's intentions for him) since before even the BbS days.