Ugh, so he's Relaxed...and his speed is barely over 100...guess I should reset...but...having to do that whole fight again after...ugh...
Here's a couple of hints to get a good one faster.
1. Kill the Yveltal / Xerneas. When you do that, it'll actually come back immediately and stay here like a normal legend. Natures and IVs aren't set, so you can do this to avoid that cut scene every time!
2. Get a Pokémon with the Syncrhonize ability (like Ralts or Abra) with the nature you desire, and have it fainted but in the first slot of your party. This gives you a 50% chance of getting the nature you want. In Yveltal's case, you have a lot of choices. You can use Timid for the pure special set, or Modest if you want more power and bulk. Hasty is good if you want the mixed set with Suckerpunch, or the Acrobatics set. Finally, if you want a defensive Yveltal, go for a Calm nature.
Xerneas is pretty offensive. Modest is probably the best, but if you're a speed freak like me and want to outspeed Rayquaza when they come back, you can use Timid. Hasty / Naive may also end up being good for a Choice Scarf set with Megahorn (for Mewtwo and CM Latias) and a possible Life Orb set with Close Combat.
3. In the case of Speed, bring a Pokémon who is ONE speed point lower than Xerneas / Yveltal. For reference, a perfect speed neutral nature one has 119 Speed, while a +Speed nature one has 130 Speed.
4. Finally, bring 3-4 rare candies and a Reset Bag. after you do that other fight, use the Reset bag to get rid of all the EVs from that battle. Use the rare candies and this IV calculator:
http://www.metalkid.info/Pokemon/Calculators/IV.aspx
I'm not sure if they got the other Pokémon accurate, but I can say that they have Xerneas and Yveltal's stats spot on!