Golduck
Did you expect to see Golduck here? Yes? Okay then. Golduck's Cloud Nine is an amazing ability, especially factoring in Primal Groudon's 4x weakness to Water, and Mega Rayquaza's 4x weakness to Ice. The weather conditions they have would normally block out those weaknesses, but Cloud Nine does in fact negate the primal weather, and so a Modest, Scarfed Golduck can OHKO Mega Rayquaza 93.8% with an Ice Beam, and Extreme Speed, even at +1 with a Life Orb, only has a 31.3% chance of OHKOing Golduck.
252+ SpA Golduck Ice Beam vs. 0 HP / 0 SpD Mega Rayquaza: 348-412 (99.1 - 117.3%) -- 93.8% chance to OHKO
+1 252 Atk Life Orb Mega Rayquaza Extreme Speed vs. 0 HP / 0 Def Golduck: 266-315 (88.3 - 104.6%) -- 31.3% chance to OHKO
Now, those are a few things that could possibly remove Mega Rayquaza. I'd like help coming up with hard counters.
While you are at it, you could list regular Rayquaza with its similar ability and access to
Ice Beam, but there is the possibility of Scarfed Mega-Rayquaza KOing it instead.
So with its MASSIVE offenses on both spectrums and well-rounded stats, I doubt there is a true counter for it.
Thankfully, the tier it is restricted to (Anything Goes) allows cheap strategies to use. This means that sleep spam, evil evasion techniques, OHKO moves, no species clause is fair game.
Also, he's not so gamebreaking in a doubles environment (but no less dangerous). You can gang up on it with certain team combos such as Darkrai's
Dark Void and Rayquaza's
Ice Beam for a quick KO, or throw a Mega-Glalie's
Explosion just to take it down while preventing it from KOing it using a partner with
Fake Out or
Follow Me/Rage Powder. The problem though is how its partner supports its teammate.
Two good teammate classifications are those that take advantage of Mega-Rayquaza's ability to null super-effectiveness against flying and those that cover Mega-Rayquaza's weaknesses for synergy.
Tornadus I/T
As the sole mon with only a Flying Typing, partnering it up with M-Rayquaza effectively gives it zero weaknesses whatsoever. Incarnate has the benefit of throwing Priority moves like
Taunt to disrupt status moves such as Darkrai's
Dark Void or
Tailwind to double M-Rayquaza's already impressive speed. Therian has
Regenerator to recover health it tanked.
Zapdos/Thundurus I/T
By factoring strong winds, the Electric/Flying mons are also left with no weaknesses, unless
Roost is used, which leaves Zapdos with a ground weakness. Zapdos has the advantage of learning
Defog and is bulky enough to tank multiple hits and heal with
Roost. Thundurus-I possesses similar strengths to Tornadus-I but is only good for taunting. Thundurus-T is just a powerhouse.
Togetic/Togekiss
The Togepi line is only notable for learning
Follow Me, which has the equivalent speed priority to Fake Out/Extreme Speed to take hits meant for M-Rayquaza. With strong winds, it is left with the standard Fairy-type weakness. However, it can still put a dent on attackers with paraflinch hax.
Darkrai
While it doesn't benefit from strong wind, it can still eliminate threats to M-Rayquaza with its especially deadly movesets.
Dark Void is obvious enough, but it also carries
Ice Beam for other dragons,
Sludge Bomb for Fairies, and
Focus Blast/Incinerate for Ice and Steels.