I've played 331 matches in the Standard format on PTCGO since Sept. 1, and the three decks that have performed best against me are Volcanion EX (with Volcanion and Flareon EX), Darkrai EX (with Giratina EX or Yveltal EX), and Mega Rayquaza.
In 11 matches, Volcanion EX with Flareon EX has gone 9-2 against me. In 8 matches without Flareon EX, Volcanion is a pedestrian 3-5 against me.
Darkrai EX overall is 13-3 against me. Darkrai EX has been paired most frequently with Yveltal EX and Giratina EX. In 7 matches with Yveltal EX, it's 6-1 against me; in 7 matches with Giratina EX, it's also gone 6-1 against me. There have only been 2 matches I've played where Darkrai hasn't been paired with Yveltal or Giratina, and it went 1-1 in those two matches. Giratina and Yveltal must have something against each other, though, as no Darkrai deck has carried both of them.
Mega Ray has gone 16-4 against me, but it's worth noting that all 4 of those losses came against my Rainbow Road deck. My Rainbow Road went 4-2 head to head with Mega Ray. It's also worth noting that outside of Rainbow Road, it only went up against my other top performing decks twice (M Mewtwo and a Vespiquen Regice Glaceon EX deck). This means that 12 of the 20 times I faced it, I was playing a deck that has not fared well in this new rotation (for example, it has 3 matchups with Typhlosion, two with Sceptile, and two with a Garchomp Talonflame deck).
Also worth noting is that my 3 best performing decks have been a Darkrai EX Giratina EX deck, a Mega Mewtwo EX Garbodor deck, and the above mentioned Vespiquen Regice Glaceon deck (which I have subsequently shelved with the introduction of Karen into the meta).
Mega Mewtwo against me has been less than mediocre as it has won only 12 of the 25 matches in which I've gone up against it, but I've actually only seen the Garbodor version 7 of those 25 times. My Mega Mewtwo Garbodor deck has won 37 of 53 matches (70%).