Threat:
Xerneas @ Power Herb
Ability: Fairy Aura
Nature: Modest
EVs: 252 SAtk/252 Spd/4 HP
Moves:
- Geomany
- Moonblast
- Psyshock
- Thunderbolt/Flash Cannon
Let's get the obvious one out of the way - Power Herb Geomancy Xerneas. The only downside of this is that Xerneas has a better physical move set, but no physical Fairy attack (aka no Play Rough). Anyway, if you let this thing get a Geomancy off, it can tear through entire teams.
Counter:
Excadrill @ Life Orb/Choice Scarf
Ability: Mold Breaker
Nature: Adamant
EVs: 252 HP/252 Atk/4 Def OR 252 Atk/252 Spd/4 HP
Moves:
- Iron Head
- Earthquake
- Rock Slide/Stone Edge
- Shadow Claw/Brick Break/Rapid Spin
As a counter, Excadrill is pretty good. It resists all of the moves on special Xerneas, and hits back with a Super-effective STAB Iron Head. Also, a counter is only useful if the Pokemon can also function well in the tier. Considering Excadrill was Ubers in Gen V (I don't know what it is in Gen VI) it can also do some work, and as a bonus is one of the few good Rapid Spinners in the tier.