You seem to be a bit confused as to what the difference between a check and a counter is. A counter is a Pokemon that can consistently and reliably switch into the majority of a Pokemon's sets, and beat it 1v1. A check is a Pokemon that, while it generally wins 1v1, struggles to consistently switch in or loses to a common variant of the set. You said that Mega Ray is a counter to Mega Gengar, but this is not the case. While it is true that Mega Ray can switch into Mega Gengar and not be OHKO'd and then OHKO MGar in return with Espeed, it isn't a counter because it takes like 75% to do so. It can't switch in more than once, and it can't switch in at all if its taken a bit of prior damage. An example of a counter to Mega Gengar is PH Yveltal, which can easily take even boosted hits from Mega Gengar, recover off the damage, and OHKO with Knock Off. Yveltal can deal with Mega Gengar consistently and repeatedly; this is what makes it a counter, rather than a check.
Now that thats cleared up, I want to look at Protean Mewtwo Y. You've talked before about M2Y's supposed counters, and I want to examine that. What counters Protean M2Y? First, lets evaluate the standard and most common set, Spooky Plate Judgment/Secret Sword/King's Shield/Boomburst|Quiver Dance|occasionally Sludge Bomb. Here's a list of every somewhat viable counter I could come up with.
Mega Audino can beat many variants of this set, but it loses to Sludge Bomb and it's very shaky against Boomburst sets.
252 SpA Protean Mega Mewtwo Y Boomburst vs. 248 HP / 252+ SpD Mega Audino: 190-225 (46.4 - 55%) -- guaranteed 2HKO after Stealth Rock
Additionally, SpDef spreads can be 2HKO'd by +1 Secret Sword.
Magic Guard SpDef Ho-Oh does generally counter this set, but it's 2HKO'd by +1 Judgment and can't OHKO M2Y in return, making it a bit shaky. In any case, SpDef Ho-oh is a fairly niche set that was literally devised specifically to beat M2Y. It would likely get very little usage if Protean M2Y weren't around, so the prevalence of this set I would argue is testament to Protean's centralisation of the meta more than anything.
Fur Coat Chansey is probably the most reliable counter to this set, but even that has to play 50/50s against Quiver Dance+Secret Sword sets. Regardless, FC Chansey is quite possibly the most passive, momentum-sucking Pokemon in the tier, and it really isn't the sort of Pokemon that most teams want to be running; the fact that so many offense and balance builds are slapping on FC Chansey just to cover Protean (and other miscellaneous threats) is honestly pretty gross and really says a lot about the sorry state of the current meta.
Shedinja does beat this, but we all know how unreliable Shed is a counter to anything.
Yveltal does decently, but depending on its spread it struggles to take Secret Sword or Boomburst, especially with Stealth Rock up.
The only decent RegenVest Pokemon that can take this on is Xerneas, as all of the others are either weak to Judgment or don't have the bulk to take Secret Sword. However, even this has to run a subpar Specially Defensive spread or it risks being 2HKOd by Judgment after rocks, and in any case this is an extremely uncommon set. And, similar to Ho-oh, this is a set that exists specifically because Protean M2Y is so prevalent, and as such I'm kinda reluctant to list it as a counter to it seeing as its a set that basically wouldn't be used if Protean weren't around.
That's it. Every other at-least-somewhat-viable Pokemon in the tier cannot stand up to Judgment + Secret Sword. That is a grand total of 6 Pokemon, all of which have to be at close to full health to avoid being 2HKO'd switching in, all of which can lose to fairly common coverage options, the majority of which are passive, defensive Pokemon that don't really fit onto most teams that well, 2 of which are used almost solely because they can counter M2Y, and one of which is Shedinja which is extremely unreliable. That is an extremely sparse and inconsistent collection of counters. And that's not even mentioning its other sets! The Life Orb set that
bp scrub brought up beats basically all of these Pokemon, the Earth Plate set can beat quite a few, and the Tail Glow set that I used against
InfernapeTropius11 in the BH Open
here can beat most of M2Y's standard counters pretty easily too - in this replay it gets past an FC Chansey, a SpDef Ho-oh,
and a MAudino, all of which were at full health.
Now, you could argue that this is not something unique to Protean, that any offensive Pokemon in BH can beat its usual checks and counters with particular coverage moves, and you wouldn't be wrong. Mega Gengar can pack Sludge Bomb to beat MAudino, PH Kyogre can run King's Shield to avoid being revenge killed by -ates, etc. However, the difference between these examples and Protean is that these Pokemon have to sacrifice something to run these coverage options, whereas Protean - by virtue of the fact that it already beats like 95% of the tier with 3 moves - doesn't really lose any functionality when it slaps on some random coverage move. I'll use Mold Breaker Mega Gengar as an example. The standard set is Spooky Plate Judgment/Secret Sword/Pursuit/Shell Smash|Quiver Dance. If Mega Gengar wants to run Sludge Bomb to hit MAudino, it has to sacrifice an important move to do so - if it drops Pursuit then it can't trap Shed, if it drops its boosting move then it has trouble sweeping and can't break through a lot of mons that it would be able to otherwise, and if it drops Secret Sword then it loses the ability to get past Darks and Normals. There's an actual tradeoff there; MGar is sacrificing functionality in order to beat MAudino. On the other hand, M2Y doesn't sacrifice anything by slapping on Boomburst, or Sludge Bomb, or Quiver Dance, or Tail Glow, or Infestation, or Spore. It achieves what it needs to with just 3 moveslots, and the fourth is completely free, just icing on the cake. This gives Protean a truly unparalleled level of versatility, and this in my opinion is the crucial factor as to why its worthy of a ban.
To recap: Protean M2Y beats the vast majority of offensive Pokemon 1v1 due to its phenomenal speed tier, immense power and ability to run perfect coverage unimpeded by its typing. This forces every team to run defensive counters to it, because offensive checks are practically non-existent; yet M2Y has a pathetically small list of supposed counters, and every single one either loses to common variants, is extremely passive and thus poorly suited for most team archtypes, is mediocre outside of beating M2Y, or some combination of these. Additionally, M2Y can customise its set to effectively pick and choose its counters without hindering its ability to perform its usual roles, which overall means that teams generally have to run multiple checks and counters to M2Y to avoid just getting blown away by it (and even this is sometimes not enough). This is making the metagame extraordinarily centralised, it limits the potential for variety and creativity in teambuilding, and generally makes the tier less fun to play (I'm fully aware that that last one is a purely subjective judgement). And this isn't even to mention the other viable Protean mons: M2X, which does most of the same things as M2Y but with a worse speed tier and less ability to run anti-Imposter sets; Mega Latios and Mega Rayquaza, which are even harder to wall than M2Y at the cost of some speed; and other miscellaneous niche Protean mons which can be used to lure in specific defensive Pokemon. Protean has a stranglehold on the metagame, and tbh I can't wait to be rid of it.
Now, some nitpicking:
Literally not one of these examples is relevant. Levitate steels are extremely uncommon and generally fairly mediocre, and they have been since the release of TArrows. PH Ho-oh is shit and nobody ever uses it - and in any case it gets clean OHKO'd by this M2Y set if rocks are up. bp scrub mentioned both Chansey and Shedinja as exceptions in his post. Max SpDef AV Regirock under sand is hardly a common threat in BH, and the fact that this mon has a very solid chance to 2HKO a fairly bulky, fully SpDef invested Pokemon at what is effectively +2 SpDef is a testament to how broken it is more than anything. Sand TTar is 2HKO'd (unless this one is AV too):
252 SpA Life Orb Protean Mega Mewtwo Y Earth Power vs. 252 HP / 252+ SpD Mega Tyranitar in Sand: 218-260 (53.9 - 64.3%) -- guaranteed 2HKO
Cresselia is barely a relevant Pokemon in current BH, and its 2HKO'd by Boomburst anyway. The only really common Soundproof mon is MSlowbro, which gets nearly OHKO'd by Moonblast, and there are no other Soundproof Pokemon relevant enough to be used as a true counterargument here.
Also, completely irrelevant aside: using decimate to mean destroy is not improper usage. Language is ultimately defined by how its speakers use it, and the vast vast majority of english speakers use the word decimate to mean 'destroy' and have done so for hundreds of years; it hasn't meant 'to remove one tenth' for a very long time. Correcting people when they say this makes you seem like a pretentious twat.