No, you have to catch it before you can move on from there. If you try SR'ing for Nature with IV's, lots of other topics have listed what the "observed erfect stats" are when you check its stats in the summary screen. I don't have the numbers onhand.
If you faint Xerneas the very first time you fight it it will respawn immediately, but you get the opportunity to save before challenging it again (so you won't have to see that tedious cutscene again). After that just catch it, finish the boss battle, check its IVs/Nature and reset if they stink.
3DS FC 4511-0567-3041 (Boldore, Magcargo, Rhydon) Martijn - inofficial pesky Claw using git of Kid Icarus Uprising's online modes
You don't even have to beat the boss, you can check its stats in the summary and run it off an IV calculator, barring the random nature screwing up your calculations, which is why I recommend Synchronise, since as long as you constantly get the same Nature and take note of the apparent 31's in its IV's, you can tell off the bat when you have the right Nature and good IV's.