First, a prelude.
In an Uber Team you need someone to check both Kyogre and someone to check ExtremeKiller Arceus. It’s fine if you don't have checks for anything else, but those two are so common and so dangerous that every team needs a check.
Kyogre looks good as you have it, Classic CM + 3 Attacks. You might consider changing Surf to Scald, as it will still pack a punch after a few CMs yet still have the chance to burn physical attackers who threaten your unboosted Defense.
For Rayquaza, I'll give you some pointers. Rayquaza does not function well as a Choiced pokemon due to constant switching, yet without the Choice item he lacks the power to get the KOs. This is why he makes such a beautiful Life Orb user. Secondly, you mentioned Air Lock but you're not taking full advantage of it. I like using it against opposing Ferrothorn in rain. And Overheat works better than V-Create as it requires no investment and means you won't have any stat drops (assuming the rest of your attacks are physical, if not Fire Blast is also an option).
So let's make these changes.
Rayquaza @ Life Orb
Trait: Air Lock
EVs: 252 Atk / 252 Spd / 4 HP
+Atk -SDef Nature
- Swords Dance
- Extremespeed
- Dragon Claw/Outrage
- Overheat
You biggest worry with using this fellow, is how quickly he can die. When you bring him in to play, it's always better to have him in a position where he's likely to get a Swords Dance up. Then you stand a good chance of KO'ing some opposing pokes. Bringing him in on Ferrothorn and expecting a switch is a really bad idea, Overheat immediately, and if they switch you can always switch out the next turn. Outrage works better at the clean up stage of the game, but the next suggestion fills that role, so you may want to use this guy as a suicidal wall breaker.
While he's a great pokemon Mewtwo doesn't really do anything for the team.
Mewtwo's replacement:
Kabutops makes for a great physical rain cleaner. He can also double as a Spinner for the team. Being a rock type means that at full health he can go up against a 70% Arceus normal and take it out before it fires off an Earthquake.
Kabutops @ Life Orb/Lum Berry
Trait: Swift Swim
EVs: 252 Spd / 252 Atk / 4 Def
Adamant Nature
- Stone Edge
- Waterfall
- Low Kick
- Rapid Spin
Waterfall in rain is perfect for cleaning up the remainder of that opposing team, coupled with wickedly powerful Stone Edge you get nice Dual STABs. Low Kick is almost necessary, able to take out Arceus-Normal, Dialga, Ferrothorn and, Steel types in general. Rapid Spin is there for spinning allowing you to switch in and out with more ease. Life Orb will allow you greater power whereas Lum means you can come in against Giratina and suck up a status in return for the KO. It depends on which situation you find yourself in more often:
You get haxed a lot or find that Kabutops is receiving a lot of status = Lum Berry
You need to deal as much damage as possible = Life Orb
Now to talk about walls. We still need a hazard setter for the team and while I was thinking Forretress, Ferrothorn fits the bill better with its Electric resistance. It works dangerously well in Uber Rain teams with its Fire weakness reduced. In this instance it will work better as a physical wall to absorb hits for Kyogre.
Ferrothorn @ Leftovers
Trait: Iron Barbs
EVs: 252 HP / 252 Def / 4 SDef
Impish Nature
- Leech Seed
- Stealth Rock
- Thunder Wave
- Power Whip
You'll find most people prefer investing EVs in Ferrothorn's SDef, but I like using Physically Defensive Ferro in Ubers. It can take hits from +2 Arceus, so long as it's not carrying Brick Break.
+2 252+ Atk Life Orb Arceus-Normal Earthquake vs. 252 HP / 252+ Def Ferrothorn: 175-207 (49.71 - 58.8%) -- 69.53% chance to 2HKO
Leech Seed is great for stalling out opponents and paired with Leftovers you'll be getting health in no time. Thunder Wave is wonderful for crippling opponents like Palkia, who gets a 2HKO in rain if carrying Fire Blast,
252 SpA Palkia Fire Blast vs. 252 HP / 0 SpD Ferrothorn in rain: 256-304 (72.72 - 86.36%) -- guaranteed 2HKO
Meaning you can get a TWave off which ruins it as a Revenge Killer. Power Whip is in case you end up Taunted. Also good for dealing some heavy damage, especially against the weather setters TTar, Hippodon, Kyogre, and Groudon. Stealth Rock is your hazard for the team.
Now, You have a Weather setter, a Spinner/Cleaner, and a Physical Wall. Next up is a Spin Blocker and additional wall. While the only hazards you're using are Stealth Rocks they are still important to have as they deal some heavy damage to several Uber pokemon, such as Ho-Oh, Reshiram, Shaymin-S, and more. Plus, a Ghost type happens to work quite well for the team.
Arceus-Ghost can fulfill many roles as well as managing to check one of them most dangerous Uber threats, Ekiller Arceus. It can function as a spinblocker with its typing alone, and a wall with its vast movepool and stats. With Ferro acting as your Physical wall, GhostCeus can act as your Special wall.
Arceus-Ghost @ Spooky Plate
Trait: Multitype
EVs: 248 HP / 252 SDef / 4 Spd
Calm Nature
- Will-O-Wisp
- Roar
- Recover
- Judgement*
Classic Special wall with WOW to take down physical attackers. Your main check for Arceus, either Will-O-Wisp if they haven't set up (Lum Berry) or Roar if they have a Swords Dance set up. Recover is fairly obvious, Judgement is powerful STAB. The set can't effectively take down Blissey or Chansey so get out of there if you see them coming in, you could also Roar them out.
Last but not least, your backup Scarfer. Palkia works very well under rain as both a Kyogre check and a killer. Equipped with one highly dangerous Spacial Rend, and a Thunder of its own you’ll be hitting everything. Fire Blast is a must for Forretress and Ferrothorn, while the last moveslot is granted to a STAB water move Surf for accuracy or Hydro Pump for overkill. You can alternatively run the same set but give Palkia a Lustrous Orb, which is arguably the better set. With Kabutops acting as your Scarfer under rain, Palkia is free to spam Thunders and Spacial Rends to its heart’s content. The problem with running this set however, is if you lose the weather war, then Kabutops will fail, as it relies upon rain for speed. I’ll give you both sets, and you can try both.
Palkia @ Choice Scarf
Trait: Pressure
EVs: 252 SAtk . 252 Spd / 4 HP
Timid Nature
- Spacial Rend
- Thunder
- Hydro Pump
- Fire Blast
Palkia @ Lustrous Orb
Trait: Pressure
EVs: 252 SAtk . 252 Spd / 4 HP
Modest Nature
- Spacial Rend
- Thunder
- Hydro Pump
- Fire Blast
That’s what I would do for your team, I apologize for taking so long to finish writing this rate, but better late than never. Hope this works well for you and good luck in your future endeavors!
~MrK