#5 Put aside Legendaries, Pseudo-Legendaries, and Mega Evolutions
Legendary Pokemon are legendary for a reason. The stats of Xerneas and Yvetal, the mythological mascots of Pokemon X and Y respectively, far exceed that of the majority of the Pokemon you'll meet through your adventure. Since you encounter these legendary creatures throughout the course of the story, it's mighty tempting to slot them into your party and use them to crush every trainer you meet afterword.
Keep those mythological beasts of PokeLore locked up inside your PC storage system and out of your party. Doing so will make the battles ahead a lot less one sided without what essentially amounts to a God or Deity on your side. While you're at it, ditch pseudo-legendary Pokemon, which include most three-stage dragon types like Dragonite, Hydregion, and Goodra, and avoid using the newly introduced Mega Evolutions as well. Mega Evolutions power Pokemon up to be on-par or stronger than many legendary Pokemon in X and Y, and a well-trained Dragonite can wreck just about any opponent.