I've already got two Megas on my team, Mega Mewtwo is out. Considering the the environment I'm expecting, I've got two items for consideration: Colbur Berry and Assault Vest. The former allows Mewtwo to survive a Sucker Punch or even a Dark Pulse from Yveltal and deal some hefty damage in return. It will still likely fall before taking it out, though. The latter gives it a solid chance to survive a Power Herb Xerneas' Moonblast after Geomancy, and potentially 2HKO it. Here are some calculations:
+2 252 SpA Fairy Aura Xerneas Moonblast vs. 0 HP / 4 SpD Assault Vest Mewtwo: 303-357 (85.8 - 101.1%) -- 6.3% chance to OHKO 252 SpA Mewtwo Psystrike vs. 4 HP / 0 Def Xerneas: 195-229 (49.4 - 58.1%) -- 98.4% chance to 2HKO
This means that if they're sent out on the same turn, Xern with use a turn to Geo, tanking a hit. It will then Blast Mewtwo, who has a solid chance for survival and KO it back with high a likelihood.
252 SpA Life Orb Dark Aura Yveltal Dark Pulse vs. 0 HP / 4 SpD Colbur Berry Mewtwo: 251-296 (71.9 - 84.8%) -- guaranteed 2HKO 4 Atk Life Orb Dark Aura Yveltal Sucker Punch vs. 0 HP / 0 Def Colbur Berry Mewtwo: 208-246 (59.5 - 70.4%) -- guaranteed 2HKO 252 SpA Mewtwo Thunderbolt vs. 0 HP / 0 SpD Yveltal: 226-268 (57.5 - 68.1%) -- guaranteed 2HKO
This shows that one on one, Yveltal will still win (unless it lacks Sucker Punch for some reason), but Mewtwo can take off a big chunk of health before going down.
I'm running a Mega Scizor and a Sucker Punch Yveltal myself (albeit of a hindering nature), so I have revenge killing possibilities. Now...I'm honestly expecting Xerneas to be the more common threat. I do have my Mega Scizor to help with it, but once it gets rolling it can really screw you over. I don't have a lot to help with Yveltal, though. Colbur pretty much ONLY works for Yveltal and MegaMawile, while AssVest has more utility.
I'm still leaning towards the AssVest because of fear of Xern. I don't expect as many Yveltals, but it's also a significant threat - one I lack decisive means to counter. For the record, the team I've planned is: - Mewtwo - Yveltal (Life Orb) - Megazard Y - Mega Scizor - Sableye (Leftovers) - Gyarados (Intimidate; Lum Berry)
Being limited to Kalos pokes and not wanting to succumb to Talonflame/Aegislash/Rotom doesn't provide many options :/