What's annoying is that, in the end, the reason they made MegaEvos was because they wanted to make 4-stage mons yet didn't want to break their self-imposed rule, so they went with the "glorified formes with unifying lore" route they now want to abandon forever as a gimmick. I don't think they can easily solve this unless they just decide to make 4-stage mons, or just retcon old pokemon designs.
The 2-stage mons could be solved with some sidequest in a future game (like the DP remakes lmao never) where a Professor is trying to ease the effects of the MegaStones and turn them into permanent form changes. He'd then name the new "species" as a normal mon and, for all effects, from that point on in the games, that old Mega would now become an Evo. Meanwhile, Rayquaza would keep its Mega as it's part of its lore, Mewtwo could need to learn a specific move like Rayquaza (or maybe the Megas would become gender-exclusive as that shitty Genesect movie gave Mewtwo a gender) and MegaLatis could transform holding the Soul Dew.
...but now that I said it, it could be possible. Out of all the 50 MegaEvos, only 19 are from 3-stage mons: Venusaur, Charizard, Charizard, Blastoise, Alakazam, Gengar, Ampharos, Tyranitar, Blaziken, Gardevoir, Aggron, Garchomp, Beedrill, Pidgeot, Sceptile, Swampert, Salamence, Metagross, Gallade.
So the real question is, what the fuck should they do with the 3-stage mons. There are 19 of them (Venusaur, CharizardX, CharizardY, Blastoise, Alakazam, Gengar, Ampharos, Tyranitar, Blaziken, Gardevoir, Aggron, Garchomp, Beedrill, Pidgeot, Sceptile, Swampert, Salamence, Metagross, Gallade) and, short of just retconning the old designs (which would be a VERY risky move), I'm not sure of what I could suggest.
