This is my first post, so sorry if I get something wrong.
First of all, the EVs. Don't put some in all your stats- for example, if all of your moves are physical, don't bother going for Sp.Atk. For example, since your Rayquaza is a physical set, I'd put 252 Atk and 252 Spd, then put the remaining 4 in Def or something else (but not Sp.Atk because you don't have any special moves.)
Also, I wouldn't put Ice Beam on Mewtwo. I guess it could be coverage against a lot of types, but maybe Shadow Ball would be better to cover Ghost weakness and Psychic. Or you could go for Recover, so you can heal some HP back.
And Dragon Claw is perhaps not the best move for Groudon's last slot. Maybe you could go for Thunder Punch, which covers its weakness to Water and Ice, or Stone Edge, for more coverage.
Kyogre seems fine to me.
On Necrozma, I'd put Earthquake somewhere for coverage against Steel types and Primal Groudon.
For Arceus, you have an attack-lowering nature, yet you have a physical attack- Extreme Speed. I'd say to either go one way or go the other, or have a +SpAtk -Def nature. For my Zap Plate Arceus, I have Judgment, Ice Beam, Flamethrower and Earth Power (all special attacks with a Modest nature).
Hope this helps :)
