My explanation: Although Hoopa has astronomical offenses, it has a typing leaving it 4x weak to possibly one of the most common physical moves: U-Turn. It also sits at base 80 Speed, and most U-Turners are fast Pokémon like Tapu Koko, Landorus-T, and if playing Nat Dex, Dragapult. It is also walled and/or destroyed by Clefable, Azumarill, Mega Mawile, Tapu Koko, Tapu Lele, and Mega Diancie. Volcarona, Mega Scizor, & Mega Pinsir all threaten it with powerful 4X Bug STAB. Oh yeah, base 60 defense is pathetic.
Oh, and here's smogon's explanation:
Hoopa-U is one of the strongest wallbreakers in the tier due to its incredible offensive stats and typing that allow it to threaten a majority of defensive and balanced teams with its STAB moves and great coverage. Its high Special Defense stat also allows it to check the likes of Gengar and Latios from full HP, although Hoopa-U should not be used as a primary check to these special attackers. On the flipside, its middling Speed stat, despite being good for a wallbreaker of its caliber, leaves it at the mercy of a number of faster offensive threats in the metagame such as Greninja and Tapu Koko. It also carries poor physical bulk along with a 4x weakness to one of the strongest momentum gaining moves in the game, U-turn, meaning that Hoopa-U tends to get overwhelmed by the likes of U-turn Tapu Koko.
TL;DR: Hoopa is good at breaking down stall and balance, but like Mega Garchomp, it gets outsped and destroyed by many of the metagame's top threats.
Hope this helped!