I'd say that the largest drawback to a Mega Stone is that the Pokemon can't heal itself, power up or cure status with items. However there are other ways to achieve this. To heal up your Megas you can use a Wish passer. You can cure status using a cleric. And to boost stats you can use moves like Swords Dance or Dragon Dance. So everything you lose out on by using a Mega Stone you can regain by using your teammates or moves instead. The Mega evolutions have better stats and can often pull off a single handed sweep by setting up. So no, I would say it's worth using your Mega stones even thought it'll be difficult to change your battle style, because in the end it'll benefit your teams tremendously.
