Question

Deoxys(D)@Red Card
Trait:Pressure
EVs:252HP,128Def,128SDef
Nature:Calm
Role: Staller/Setup

• Toxic
• Recover
• Cosmic power
• Stealth rock

So, Deoxys is a classic staller which can setup stealth rock, which helps onto countering Multiscale Lugia. Red card helps him when the foe has throw out a heavy enemy wich cannot be killed with Toxic. Recover has PPmax since I'm using too much. Cosmic power increases Deoxys' enormus attack and makes him very difficult to kill. Another option instead of Stealth rock is Night shade since he may get taunted.

Kyogre@Chesto berry
Trait:Drizzle
EVs: 252 HP, 128SDef, 128SAtk
Nature:Modest
Role: Wall/Setup

• Calm mind
• Rest
• Thunder
• Water spout

With this one I set up rain and I take some advantages. I picked-up Thunder instead of Ice beam since Kyogre will have problem against other Kyogre ot Lugia. Its basic strategy is a chesto-rest strategy wich lets him boost while recovering HP.

Manaphy@Life orb
Trait:Hydration
EVs:252Spd, 252SAtk, 4HP
Nature:Timid
Role:Special Sweeper

• Tail glow
• Rest
• Surf
• Ice beam

The ultimate rain abuse. I boost one or two times with tail glow, then I rest, and for Ending I kill everything with surf.
I used to have Grass knot in last place, but I switched it with Ice beam since I nead a bit more Dragon-killing.

Zekrom@Leftovers
Trait:Terravolt
EVs:252Atk, 252Spd, 4HP
Nature:Jolly
Role: Physical sweeper

• Hone claws
• Bolt strike
• Stone edge
• Dragon claw

This nice sweeper is Lugia's and Kyogre's Counter. It hits them with 2x power (Bolt strike) and the nice thing is that those damage are physical. After two hone claws he can defeat anything.

Latias@Soul Dew
Trait:Levitate
EVs:18HP,128Def, 252Spd
Nature:Timid
Role:Special Tank

• Calm Mind
• Mist ball
• Surf
• Dragon pulse

A tank which takes some turns to boost with calm mind and then he has great Bulk as well as Speed. Also some rain abuse is made due to Surf. Dragon pulse is STAB and helps to the countering of dragons which have no weakness to Ice such as Palkia and Reshiram...

Darkrai@Focus sash
Trait:Bad dreams
EVs:252SAtk, 252Spd
Nature:Timid
Role: Sleep Sweeper

• Dark void
• Nasty plot
• Ice beam
• Dark pulse

Dark void, Few nasty plot boost and then he destructs whatever he finds in his path. Dark vid also helps him onto sweeping and ability abuse.

Answer 1

Not bad. All I would suggest is that you take out Nasty plot on Darkrai and replace it with either Thunderbolt or Dream Eater, your choice. T-Bolt to have Bolt-Beam coverage, or Dream eater for fighting type coverage and to make the most od the sleep. Hope this helps :)