Origin Shards
Okay so- one of the biggest issues I've had with switching around the timeline/ making one singular timeline (there's many but this' one of the more obvious ones) is the 'Mega timeline', where ORAS happens after XY- But! I think I've found a solution for that. (*Note: I haven't played Oras... yet)
As the title reads- I've thought up of Origin Shards! Basically, yaknow how mega stones all kinda look like marbles? Well, Origin Shards are the unrefined/raw version of mega stones! Just straight shards from the meteors that Rayquaza breaks*; so kinda like how wishing stars are. Origin shards can still be refined into the stones- but at the time they just weren't known as Mega Stones. It's obvious where I got the name from lmao (Rayquaza should've been named Origin not mega-)
Origin Shards were originally found in Hoenn; but instead of being something brand new like how Mega-evos are in XY, Origin Shards are more of a common thing- they're still fairly rare, but not as rare as in XY (Where only the player gets a key stone, and the mega stones are hidden.)
Now when it comes to the professors Birch and Sycamore; I'm thinking that maybe Birch (who's field is in pkmn habitats) either already had his field, and couldn't focus on the OS/MS; or he assumed that Origin forms mattered due to habitats, rather than the shards themselves. Regardless, it wouldn't be until years later when Sycamore took up researching them directly- when they also started to appear in Kalos.
sorry for the ramble; I hope this makes sense lol