tl;dr
Mewtwo's set #1 should have Psychic as a secondary option at best, not a requirement. Sure, it gets STAB, but that's about all it does. Seriously, what is Psychic going to hit harder in ubers than the combination of Thunderbolt and Ice Beam? Blissey is about it, which beats non-taunt/101 HP sub Mewtwo's, anyway.
A 101 HP subber is played totally differently from two attacks CM recover, so that they probably shouldn't be the same set. It should be split into two sections, one with Calm Mind, Recover, Thunderbolt, Ice Beam, the other with Calm Mind, Recover, Substitute, Psychic/Ice Beam (Psychic for STAB, since it's your only attack, Ice Beam to hit nearly all physical attackers super effective, except Metagross, which is still hit harder by Ice Beam than Psychic, since Calm Mind protects you from special attackers). Secondary options for that set would be Thunderbolt+Ice Beam (only use together with two attacks imo) over Psychic and Recover.
Set #2 should mention that Tyranitar is rare in ubers, and Blissey isn't as common as one would think, either.
Set #4 should have Ice Beam as another option over Psychic, both are good, for reasons I said in the 101 HP subber thing... Ice Beam hits the physical attackers--Groudon, Rayquaza, Lugia, Deoxys-F, and Metagross--Harder than Psychic, while CM protects Mewtwo from special attackers like Kyogre. It's not as biased in favor of Ice Beam as with WW Lugia, though, because Mewtwo can't take Kyogre surfs, for example, nearly as easily, but if it gets in a CM or two with Recover, it might work. Ice Beam is also nice for not having any immunities, but it's not like dark types are that common.
Lati@s:
Dragon is quite possibly the best attacking type... if you're only using one type of attack. On the multi type Lati@s--those with Thunder(bolt) and/or Ice Beam--Dragon Claw is pointless. The only Pokemon Dragon Claw will hit harder than the combination of Thunderbolt and Ice Beam are Pokemon neither Thunderbolt nor Ice Beam hits super effectively (but not Steelix, Scizor, and other dragon resisters), and other Lati@s. Oh, and Bagon! Lati@s without Safeguard, Substitute, or predicted Roars with Spikes will have real difficulties taking on Blissey, anyway, unless you don't care about being statused, which can seriously hurt this dragon. Dragon Claw can also help with Mewtwo or something, I guess, but I'd prefer HP Dark and Thunderbolt/Ice Beam, probably... Or something.
Under opinion, it should be mentioned that almost all Groudon do carry HP Bug now, due to Lati@s and Exeggutor.
Groudon:
For set 1, put HP Bug as the fourth option, and all the fire moves as secondary. Eruption sucks. Flamethrower does not OHKO Skarmory. Adamant Fire Blast has a 58% KO rate. Overheat has 100% OHKO rate, and 5% more accuracy. You'll only be using it once, really, so that would be the primary choice if you want a fire move. Liechi shouldn't be an option, as Groudon is one of the slowest Pokemon used in ubers. Salac or Leftovers are the only good choices imo. Maybe Lum Berry or something, but it's immune to paralysis, and the common sleepers beat it, anyway.
My favorite CB spread:
EVs: 252 HP / 252 Atk / 4 SDef
Adamant Nature (+Atk, -SAtk)
Especially if it's a starter Groudon. The lower speed allows you to have your weather go after Kyogre's so it's sunny. This allows you to switch to anything from Exeggutor to Lugia to Mewtwo and not worry about surf. It also survives max special attack Modest Kyogre Water Spout in the sun, and OHKOs Kyogre without HP or defense fully 3/4 of the time. In fact, Kyogre needs to devote 186 HP EVs to survive (or 116 defense EVs) for sure. I'd prefer to give it ~20% damage before attempting this, though, just in case.
Kyogre:
Water Spout does not work with Calm Mind, Rest, or in general, really. Kyogre is slow. You take hits as you CM up, and take hits on a rest. This means that Water Spout won't do the maximum possible damage. If it's used at all, it's for hit-and-run tactics, and in conjunction with Hydro Pump/Surf for when you're down on HP. A similar spread to the above Groudon spread could work on Kyogre as well, for the same reasons.
Lugia:
The whirlwind Lugia deserves its own set. Psychic isn't that good on it, either. My favorite Lugia set is CM, Recover, WW, Ice Beam, for reasons mentioned under Mewtwo. This easily doubles in power if paired with Deoxys-L with max Defense+HP, or Skarmory, as it provides both a physical tank and spikes, which are very important.
The speed it needs is 307 minimum, not 309, if you want to beat Kyogre/Groudon. I've used slow Lugia, though, too. This has the benefit of not caring about paralysis, since the way I play my Lugia always gets it paralyzed. In fact, paralysis can help it, as it suddenly becomes an amazing Exeggutor counter, since it cannot be put to sleep and resists Solar Beam+Psychic.
The EVs used for that damage calculation should be included. Uber Zapdos would use Thunder, not Thunderbolt, as well, so the first calculation isn't that important imo.
Metagross is an amazing counter to almost all Lugia sets, since one Meteor Mash attack raise on a CB Gross means GG Lugia, while the best Lugia can hope for is a predicted CB EQ, which isn't even a 2HKO IIRC.
More to come on the rest of the ubers later.