Counter - Klefki
Klefki @ Leftovers
Ability: Prankster
EVs: 248 HP / 8 Atk / 252 SpD
Careful Nature
- Play Rough
- Thunder Wave
- Toxic / Heal Block
- Spikes / Flash Cannon
Standard Klefki counters Yveltal pretty comfortably as it resists both STABs and invests fully in special bulk. It also has other uses such as being one of the most reliable checks to Xerneas (Thunder Wave). Prankster Thunder Wave also allows it to check some other set-up sweepers such as Mega Salamence. Toxic can put things it can't really hit on a timer, such as P-Don and walls in general, and Spikes is for hazard stacking. Heal Block is a decent option too to mess with walls, and also prevent Yveltal regaining HP from Oblivion Wing. Play Rough is the STAB to hit Yveltal for SE damage with, as well as break Xerneas' Substitutes. Flash Cannon over Spikes if you don't need it is a decent option too as it OHKOs Mega Diancie and hits non-geomancy Xerneas harder (use Sassy nature with Flash Cannon).
Calcs
252+ SpA Life Orb Dark Aura Yveltal Dark Pulse vs. 248 HP / 252+ SpD Klefki: 99-117 (31.2 - 36.9%) -- guaranteed 4HKO after Leftovers recovery, with a small 7.7% chance to 3HKO after SR.
252+ SpA Life Orb Yveltal Oblivion Wing vs. 248 HP / 252+ SpD Klefki: 74-87 (23.3 - 27.4%) -- possible 5HKO after Leftovers recovery, still a 5HKO after SR.
72 Atk Life Orb Dark Aura Yveltal Sucker Punch vs. 248 HP / 0 Def Klefki: 109-129 (34.3 - 40.6%) -- 50.6% chance to 3HKO after Leftovers recovery
8 Atk Klefki Play Rough vs. 0 HP / 0 Def Yveltal: 170-204 (43.2 - 51.9%) -- 7.4% chance to 2HKO
As the calcs show, Yveltal needs 4 turns to finish off Klefki, or 3 if it switches in. In the process, Klefki's Play Rough picks up a gauranteed 2HKO when factoring in Life Orb recoil. So, Klefki will always come out on top as it needs only 2 turns to finish Yveltal, where the
minimum Yveltal needs is 3, proving Klefki can switch in and still beat Yveltal.