There are actually a few Pokemon who can counter Xerneas well without being a horrible Pokemon to use in Ubers. It all depends on the coverage Xerneas has. Most Xerneas will be using Fairy+Fighting coverage along with Geomancy. But the last move they have is unable to cover everything.
Arceus-Poison: Xerneas needs Psyshock/Psychic in order to have a chance against Arceus, as it can only 3HKO it with Thunder. Meanwhile, Arceus has Poison Jab which gets the 2HKO on Xerneas without any investment. Judgement gets only a 3HKO though, so Special Arceus-Poison should probably not be used.
Ho-oh: As long as Xerneas does not use Thunderbolt/Thunder, you'll be fine, as Ho-oh is for the most part (93% of the time) 3HKOd by Psyshock, and if it uses Flash Cannon as its coverage, it stands no chance against Ho-oh. Ho-oh can 2HKO Xerneas with both Sacred Fire and Brave Bird. Beware Rocks though.
Scizor: Choice Band 252 Attack Adamant Technician Scizor with Bullet Punch OHKOs Xerneas.
These are basically the best counters to Xerneas. There are a few others, but they aren't nearly as good as these guys or would need to run sets that are not standard.