grrr..... well, you asked... Pokemaster.... so I will break it down for you...
Swampert
W/Shell Bell
Surf
Dive
Earthquake
Muddy Water
3 Water attacks, you are nuts... there is rarely a reason to have more than 1 attack type per Pokemon.... so.. drop 2. I suggest keeping Surf, but you could keep Muddy Water instead. Add Ice Beam, a nice attack to use against Grass types (double weakness, plus Ground and Water attacks are next to useless on them), lastly add Mirror Coat or Roar....
Kyogre
W\Nevermeltice
Waterfall
Ice Beam
Thunderbolt
Water Pulse
Again with the multiple Water attacks...Make Surf the only water attack, Ice Beam, Thunder (more powerfull and more accurate thanks to Drizzle) and either Rest or Ancient Power (AP is only here if you want a way to kill Shedinja). If you use Rest, hold a Chesto or Lum Berry... Also note that for battle tower and Tourneys, this pokemon is not allowed...
Swellow
Aerial Ace
Double Team
Fly
Endeavour
And for the third time in a row... now 2 of the same type attacks!!!! Drop Fly for Return (a hefty STAB attack, assuming you train it well) and let it hold Focus Band. Also note that Quick Attack (over Return) is a nice little 'gotcha' move after an Endeavor....
Flygon
Crunch
DragonBreath
Rock Smash
Sand Tomb (temporaraliy)
Not bad, but not good.... Rock Smash horrible (note that the only good HMs are Surf, and occassionally Dive/Fly).... Sand Tomb with this set, not great.... Dragon Breath, debatable... Crunch can stay...Now held item is up for grabs, anything would work... Try Earthquake and Roar, then choose between Breath and Claw for the dragon attack (Claw has more power, but a 30% chance to Para is sweet too). If you choose breath, consider holding a Kings Rock....
Latias
Mist Ball
Psychic
Refresh
DragonBreath
Again, 2 attacks of the same type.... drop Mist Ball.. Psychic is better overall... Dragon Breath vs Dragon Claw.. again both are good, here I would defenitely go Claw though... refresh is ok, but I prefer Recover here... for the last attack try an elemental attack to round out your team, like T-bolt....
I also notice there are only 5 Pokemon on your team, so you may wanna find a 6th to help round out your team... you have simular weaknesses throughout the team... 2 to grass, 3 to Ice, 2 to Lightning. Since Grass and Ice are the 2 biggest, consider a Fire Type, especially Blazekin... his Fire/Fighting type combo is good here....