Ok a few things to what people are saying.
First off when does it say megas were discovered in ORAS. Because if it was just discovered a few years or so before the beginning of the game. Then it doesnt mean megas were discovered in ORAS before XY. Cause in XY it was said that it was whats her names like great grandfather or whatever that pretty much had the first mega the mega lucario which places that way before ORAS. Meaning this could still be in the same universe and or timeline. Especially if the Pokemon Origins show is canon to the games in anyway.
Second is this
>>21878613. Which says that "MAYBE" the evolution of pokemon took a different path. Implying something different from megas AND normal evolutions happened from the evolutions we already know.