Question: Will Game Freak allow Pokemon X/Y Trainers to trade their Pokemon and Mega Stones to Pokemon Alpha Sapphire/Omega Ruby?
Answer: Yes. Because Pokemon Alpha Sapphire and Pokemon Omega Ruby are a part of same generation as Pokemon X and Pokemon Y, you'll be allowed to trade all of your Pokemon and Mega Stones from Pokemon X and Pokemon Y to Pokemon Alpha Sapphire and Pokemon Omega Ruby.
Alternatively, you can use the Pokemon Bank application to mass transfer your Pokemon, but keep in mind that items including Mega Stones can't be transferred using that application.
Image credit: Nintendo