Definately Mega Mewtwo Y. It's ranked A- in viability rankings whereas, Mega Mewtwo X is C+. Mewtwo X speed ties with m-gengar and that's bad as it becomes 50-50 on who wins if you're using Mewtwo X and opponent Gengar whereas Mewtwo y is faster than both. Mega Mewtwo Y 2hkos xerneas and OHKOs xerneas after +2 calm mind. Although mega Mewtwo Y has low defense, it can be made up by defense EVs given in smogon. Mega Mewtwo X also has unreliable STAB zen headbutt and it can miss while psystrike can't miss coming from Mewtwo Y. Mewtwo Y can also deal with non solgalium z necrozma-DM with fire blast, opening the path for xerneas.
Also, if you're going for 3vs3, you should use necrozma ultra instead of tapu-koko as you're very weak to primal groudon, which is like,
THE most common Pokémon of gen 7 ubers.
Here are your sets:
Mewtwo-Mega-Y @ Mewtwonite Y
EVs: 40 Def / 216 SpA / 252 Spe
- Ice Beam
- Fire Blast
- Calm Mind
Necrozma-Dusk-Mane @ Ultranecrozium Z
Ability: Prism Armor
EVs: 4 HP / 252 Atk / 252 Spe
- Swords Dance
- Photon Geyser
- Stone Edge
Stone edge for ho-oh. Don't ultra burst if you see xerneas on opponent team. Photon geyser is stab and for z move. E quake for primal groudon.
Hope I helped!