But what is it doing that regular two can't? Its stall breaker set is better thanks to extra bulk but if any of those are talking about bulky or CM regular two can pull that off as well. I just skimmed that and don't disagree with any except
68 Atk Life Orb Deoxys-A Knock Off vs. 0 HP / 4 Def Mega Mewtwo Y: 283-335 (80.1 - 94.9%) -- 50% chance to OHKO after Stealth Rock
but I also don't see why it fares better versus these than regular two, which is sort of the point of dropping it since it's not worth the slot. But like I said, I haven't used it much so a more qualified opinion is good.
This was the question I was about to ask until Megazard asked it first. The opportunity cost is pretty huge if you aren't gaining enough to compensate for it. And also, I feel like you overrate MMY to a degree in your analysis.
"Focus blast has a 46% chance to ohko arceus after rocks, while lumceus has only a 70% chance to 2hko it back. Focus Miss makes that matchup even worse, but this is still a coin flip."
You presume you have rocks up but your opponent doesn't. +2 Extreme Speed is a guaranteed OHKO after rocks. If both sides have rocks up, and assuming you run 252 Timid (iirc you need that to beat 252+ Darkrai) your chance to win is that Focus Blast hits and OHKOs. Mathematically, if I do have my math right, this means that you have basically
a 30% chance to win that matchup (minor note, the chance to OHKO is slightly less than what you said, at 43.8%),
a 30% chance your team has to deal with a basically full health +2 Ekiller (FM Misses),
and 40% chance a heavily injured +2 Ekiller still lives.
If neither team has rocks up, you have practically the same scenario. Thats not really what I'd call a coin flip; rather, it's quite against you. And this presumes Jolly LumCeus. While I do think Jolly Lumceus is usually the best set, it is also the one that looks like it is the most in your favor at first glance to me, which means that other matchups against Ekillers may be worse.
"Ice beam deals 76-90 to Mray, guarenteed after rocks, while Mray sometimes misses out on the 2hko back."
I'm fairly confident that Mray doesn't have to worry whether it will get a 2hko.
252 Atk Mega Rayquaza Dragon Ascent vs. 0 HP / 4 Def Mega Mewtwo Y: 334-394 (94.6 - 111.6%) -- 68.8% chance to OHKO.
Consequently,
+1 252 Atk Mega Rayquaza Dragon Ascent vs. 0 HP / 4 Def Mega Mewtwo Y: 501-589 (141.9 - 166.8%) -- guaranteed OHKO
You win if rocks are up, but otherwise you have a still-alive and boosted Mray, which could either be frustrating or death depending on the circumstances, your team, and whether Mray is holding Life Orb.
It can taunt Xern, and 2hko's with psystrike, but loses to scarf variants or xerneas that use moonblast while it uses taunt (or geo while it doesn't). Usually a win.
Even not taking into account that you lose to the Scarf set, a good Xern player will know that the MMY player has 2 acceptable options: Psystrike and Taunt. If the Xern user correctly predicts which one will be used, Xern wins. If not, Xern loses. Hinging on one prediction when both sides have 2 options to choose from seems more like a coin flip to me.
TLDR/Conclusion So you say it beats half of S rank 1v1, when it seems to me like it beats like 1 (darkrai) + 0.5 (xern, like coin flip) + 0.3 (mray, mmy absolutely requires rocks) + 0.2 (Arceus, low win probability for MMY huge risk of rampaging ekiller), which adds up to 2.
To not be too lengthy I'll just cover the A ranks briefly. They mostly seem on par to me, but...
I dont see how it "easily beats Klefki" since it has no immunity to swagger, a respectable attack stat to hit itself with, is weak to Foul Play, and is absolutely crippled by Thunder Wave, as speed is one of its biggest assets.
"beats Kyogre Primal"
252 SpA Mega Mewtwo Y Psystrike vs. 172 HP / 0 Def Primal Kyogre: 243-286 (63.2 - 74.4%) -- guaranteed 2HKO
252+ SpA Primal Kyogre Origin Pulse vs. 4 HP / 0 SpD Mega Mewtwo Y in Heavy Rain: 324-382 (91.5 - 107.9%) -- 50% chance to OHKO
252+ SpA Primal Kyogre Origin Pulse vs. 4 HP / 0 SpD Mega Mewtwo Y in Heavy Rain: 324-382 (91.5 - 107.9%) -- guaranteed OHKO after Stealth Rock
Another big general problem I see is that Psystrike OHKOs very few things, and very many things can 2HKO MMY or at least cripple it in return, limiting its opportunities to switch in and make a difference.