First of all, I'll need to define "counter" here.
Pokémon A counters Pokémon B if Pokémon A can manually switch into Pokémon B and still win every time, even under the worst case scenario, without factoring in hax.
Source
By the above, we get to know if a Pokémon A can switch into Pokémon B, survive a hit, and win against Pokémon B, then Pokémon A is dubbed as a counter to Pokémon B.
So now, what Pokémon can switch into a powerhouse like Rayquaza-Mega, survive an attack, and win? The list is, well, quite short, but I'll be going through it here.
- Tyranitar:
Tyranitar's blessed typing in Rock- / Dark- allows it to act as one of the best Rayquaza-Mega counters that you can get. It has a resistance to Dragon Ascent, which is Rayquaza's most spammable attack. With a Shuca Berry, even a +2 Earthquake can't KO it, and it can switchin into any move except for Earthquake. It can also trap Rayquaza with Pursuit, and outright KO a -1 Def. Rayquaza with Foul Play.
It also has a recovery move in Rest, which also allows it to dodge status and recover its health anytime. However, it leaves Tyranitar vulnerable to threats it's supposed to check; most notably, Mega Rayquaza can completely bypass Tyranitar when it's asleep with two Earthquakes and proceed to sweep.
But all is not well for Tyranitar also. It takes half of its health from 4 SpA Life Orb boosted Draco Meteor, which means that the next time if it tries to come in on a Rayquaza, it'll faint. This is bettered a little by it's access to Rest, but mixed Rayquaza can pose a problem for it.
Even though it is prone to wear down quickly with Hazards and random attacks, and takes a ton from Mixed Ray, Tyranitar suffices as one of the best counters available for Rayquaza-Mega. As a check, it does what it's supposed to do, that also very beautifully.
Just make sure that you don't let it eat Shuca early game till the Rayquaza is cleaned, because non-Shuca can't counter Rayquaza.
Arceus-Fairy:
Arceus-Fairy checks Rayquaza-Mega beautifully, but as a counter, it has some issues. But on the bright side, it can counter the Rayquaza depending on what move it clicks on the switchin and what set you're running.
What can happen against a Rayquaza-Mega is you switchin:
If you're running Max HP / Max Speed, and if the Rayquaza-Mega clicks Dragon Ascent on the switchin and if they're Choice Band, then you'll survive an Ascent and KO them back with Judgement. But, if they're Life Orb, then the situation becomes tense, as after coming on in an Ascent, they can finish you off with Extreme Speed. If they're Choice Scarf, then Ascent has a 91.8% chance to 2HKO on the switchin, so it totally depends on the roll.
If you're running Max HP / Max Speed, and if the Rayquaza-Mega clicks Dragon Dance on the switchin, then they can click Ascent and you'll be KOed, if they're Life Orb. If they're not Life Orb, then you survive the KO. If they click some other move, everything in point 1 applies.
If you're the bulkier spread of 248 HP / 244 Def / 16 Spe, and if the Rayquaza-Mega clicks Dragon Ascent on the switchin, you're getting 2HKOed by them if they're Life Orb or Choice Band (Rayquaza wins 1v1 here). If they're Choice Scarf, then you survive the 2HKO from Ascent on the switchin, and KO them back with Judgement.
If you're the bulkier spread of 248 HP / 244 Def / 16 Spe, and if the Rayquaza-Mega clicks Dragon Dance on the switchin, you'll survive a Life Orb boosted Dragon Ascent, and KO them in return. If they're not Life Orb, then you survive Ascent more easily and KO them.
Now, all these calcs change if we add hazards on the field, which we usually do while making checks and counters for a certain Pokémon. In Point 1, Ascant on the switchin has a higher chance to KO the Fairy if Stealth Rock are on the field. Life Orb is a 2KO with Ascent + Extreme Speed anyways, and Scarf becomes a guaranteed 2HKO on the switchin.
Because of Fairy's over-reliance on prediction, it suffices as one of the the best check to Rayquaza-Mega, but falters a little in the terms of countering it. Still, it's an excellent Pokémon overall and will surely better your matchup against Rayquaza.
- Steel- types: Pokémon like Skarmory and Celesteela can switchin on any attack, except for V-Create, that Rayquaza-Mega throws at them, and can stall it out with Roost and Leech Seed, respectively. But because these are prone to faint against Choice Band sets, and V-Create sets too, they are not "true" counters for it. This situation is somewhat resolved by running something like RocCeus, which walls the Dragon Dance + V-Create variants, and V-Create-locked Rayquaza-Mega too.
- Other bulky walls: Defensive Zygarde-C, Lugia, and Giratina are able to avoid the OHKO from Life Orb Mega Rayquaza's +1 Dragon Ascent as well as the 2HKO from its unboosted Dragon Ascent. In return, they can retaliate with either Dragon Tail or Ice Beam. Unfortunately, Lugia loses to Choice Band Mega Rayquaza, Zygarde-C gets OHKOed by Draco Meteor, and Giratina falls to both.
These Pokémon can't be dubbed "true" counters as they can't win in a 1v1 situation, but as they can cripple a Rayquaza, they're in the list.
This is the list of Pokémon that can counter, or soft-counter Rayquaza-Mega. There are lots of other Pokémon which can check it, but the question specifically asked for counters, so I didn't list them.
Also, I answered it in accordance to the AG Meta in 2015, that is, ORAS AG. But Zygarde-Complete wasn't in ORAS, so take it as a mix of ORAS and USUM.
Hope this helps!!
