I'd like to point out that two of the three retcons mentioned in the OP are all based on changes made between immediate generations; as mentioned, Feebas's alternate evolution method is a casualty of the Contest stat removal, and if Contests return, chances are so would the evolution method. So if anything new is going to be introduced, the only pogeys getting retcon'd are pogeys from Gen 5, unless it's something drastic like removing held items.
Merging the Nidos on claims they're the same species might as well be crying for the merger of Volbeat and Illumise to be under the same condition. What /should/ happen is that Nidoran M and Nidoran F should be retcon'd to having separate names. No majority is going to champion the merging of Volbeat and Illumise, so the Nidos shouldn't be any different. They already separate themselves by Nidorina and Nidoqueen being unable to breed. Oh, and the Nido lines both have different learnsets; you wanna merge those, too? They have six moves in common out of 13. Nido M doesn't learn Aerial Ace, Nido F doesn't learn Echoed Voice, and both know unique egg moves, and you really want to merge them when they go out of their way to make them pretty different while keeping them related? Change their names and it solves everything; it's less to ultimately fuck with, like reordering the dex by three spaces. (Which will not happen in the National Dex; a subsetting arrangement like any regional dex, on the other hand, shouldn't be too much to ask.)