I believe the Mewtwo forms are ranked way too low (Regular Mewtwo is C, X is C+ and Y is B+) because of their ridiculous strength and coverage. I understand there are notable checks, such as Xerneas, Necrozma DM, whatever, but Mewtwo is one of the most versatile, ridiculous attackers in the tier. Also, it has an amazing 130 speed tier, which even without a helping speed nature, can outspeed a decent portion of the metagame: especially with Mewtwo X's Steadfast. Even in some cases, Mewtwo is naturally stronger than +2 Extreme Killer Arceus, who it also outspeeds. Mewtwo is also incredibly unique compared to other special attackers, being one of few Pokemon to get a reliable special attacking Fighting type move. Also, regular Mewtwo is actually quite powerful, when comparing it to some other Pokemon in the Uber tier who possess 150 Special attack, as oppose to 154 (and backed up by life orb). As for X, while technically outclassed by Mega Lucario, depletes other threats Lucario can't handle such as Zygarde-C. As many of you reading this might know, its most common move is Low Kick, who can surprise Chansey and Blissey, thinking they had an easy counter. And for the others weak to it, that's all that needs to be said. You could run whatever coverage you want, just slap on anything alongside Low Kick and Taunt, and appropiate EV spreads. And for Mega Mewtwo Y, the strongest uboosted attacker in the game.
Mewtwo (Regular) C -> C+/B-
Mewtwo X C+ -> B+/A-
Mewtwo Y B+ -> A/A-
I don't necessarily disagree with those rises and could see Mewtwo-Y in A- and maybe regular Mewtwo higher, but I disagree with some of your points.
You say regular Mewtwo doesn't need to run Timid, but using Modest leaves it outspeed by Mega-Gengar, who can trap and revenge kill it without risking a speed tie. It can also matter against full speed Arceus formes like SD Arceus-Ground, though that's nowhere near as much of an issue.
Mewtwo getting Aura Sphere doesn't really matter too much, because it is too weak most of the time. For exemple:
(Using 216 spa because it is the spread with 40 defense that lives Shadow Sneak from Marshadow, but it doesn't affect the calculations too much)
216 SpA Mewtwo-Mega-Y Aura Sphere vs. 252 HP / 0 SpD Arceus-Dark: 200-236 (45 - 53.1%) -- 30.5% chance to 2HKO
216 SpA Mewtwo-Mega-Y Focus Blast vs. 252 HP / 0 SpD Arceus-Dark: 298-352 (67.1 - 79.2%) -- guaranteed 2HKO
216 SpA Mewtwo-Mega-Y Aura Sphere vs. 240 HP / 0 SpD Arceus: 200-236 (45.3 - 53.5%) -- 1.2% chance to 2HKO after Leftovers recovery
216 SpA Mewtwo-Mega-Y Focus Blast vs. 240 HP / 0 SpD Arceus: 298-352 (67.5 - 79.8%) -- guaranteed 2HKO after Leftovers recovery
Focus Blast's extra damage is just too useful most of the time, requiring a lot less chip damage to kill, which matters a lot because Mewtwo doesn't have the best bulk relative to some other offensive threats, so it really doesn't want to miss out on those 1/2 hit kos and take a ton of unnecessary damage/faint (it's not frail or anything, it's just that uber threats hit very hard).
Mega-Mewtwo X just has too many problems. Yes, it fares better against Zygarde than Mega Lucario, but that's pretty much it. It struggles a lot with Arceus-Fairy and Mega-Sabley, both of which get smashed by Lucario's steel STABs, and is too matchup dependent.
I also don't think any good player would switch Chansey/Blissey into a Mewtwo unless if they read you going for a coverage move, since Psystrike does this:
216 SpA Mewtwo-Mega-Y Psystrike vs. 4 HP / 252+ Def Eviolite Chansey: 288-340 (44.8 - 52.9%) -- 28.9% chance to 2HKO
216 SpA Life Orb Mewtwo Psystrike vs. 4 HP / 252+ Def Eviolite Chansey: 312-368 (48.5 - 57.3%) -- 94.1% chance to 2HKO
So that point about Mewtwo-X luring them and surprising them with Low Kick doesn't make much sense.
I would also add that Marshadow is a huge pain to deal with for the special attacking Mewtwos, because of Technician Life Orb boosted Shadow Sneak, forcing you out every time you get a kill and making Mewtwo less threatening overall. You also face competition from Ultra-Necrozma, who is a more threatening wallbreaker that can muscle past its checks more easily (though it can get trapped by Mega-Gengar after it does, while Mewtwo-Y outspeeds it).
(This is just a really small nitpick and doesn't actually matter) Mega-Mawile, Mega Rayquaza (even before you take into account Life Orb, since Dragon Ascend has 120 power) and Primal-Kyogre(thanks to the rain boost) all hit harder unboosted than Mewtwo-Y.
That being said, Mewtwo does have fantastic coverage, a STAB to get past special walls and an incredible speed tier if you are using the Y-forme, making it super threatening since it is very difficult to switch into after your opponent's pokemon have taken some damage.