>>36724469They were trying to solve three problems:
1) Revitalize the game as a whole - Pokemon has gotten very stale, and Game Freak believed they needed a new mechanic to revive the series so to speak.
2) Increase the viability of lesser-known Pokemon and diversify competitive strategies. Let's face it: Less than 10% of fully evolved Pokemon are used competitively. It's mostly the same dozen or so Pokemon in competitive formats, which are usually Legendary Pokemon or Pokemon with really high base stat totals. Game Freak created Megas as a way to increase the BST of many weaker Pokemon so they can compete with legendaries. Problem was, Game Freak also made some of the powerful Pokemon such as Lati@s and Tyranitar also get Megas, so the gap hasn't closed all too much. With that said, several Pokemon that got Megas had little to no competitive viability and were brought back from the dead with these powerful Megas. Megas all behave differently from their non-Mega counterparts, whether it is due to changed stats, typing, and abilities. Even Megas such as Garchomp, Salamence, and Latias function differently from their non-Mega counterparts, so players have to change things up to use them.
3) Create a central theme for the story. The usual "villain team wants to change world by using super-powerful legendary Pokemon" shtick has gotten old by this point. GF needed a new theme to base the story on, and they chose Mega Evolutions. The central objective of this game is to go around the region and discover the true secrets and origins of Mega Evolution. Even with Team Flare incorporating Xerneas and Yveltal into their diabolical plans, both Pokemon are still connected to the origin of Mega Evolution as a whole. So the Xerneas/Yveltal plotline is a subplot of the Mega Evollution one; it is the nexus.