No offense to the others, but their answers are kind of...bad
Aegislash
If you're going to be using Weakness Policy Aegislash, where is Autotomize? Sacred Sword should be dropped in favor of Close Combat, and you can't rely on Shadow Sneak as your only STAB move, so why not Iron Head or Shadow Claw? Considering you're going to be using Autotomize Aegislash, the EV spread should change. Aegislash has many other generally better options though, like Ghostium Z.
Aegislash @ Weakness Policy
Ability: Stance Change
EVs: 80 HP / 248 Atk / 180 Spe
Jolly Nature
- Close Combat
- Shadow Claw / Iron Head
- Swords Dance
- Autotomize
Aegislash @ Ghostium Z
Ability: Stance Change
EVs: 80 HP / 252 Atk / 176 Spe
Adamant Nature
- Shadow Claw
- Swords Dance
- Shadow Sneak
- Close Combat
Mega Charizard Y
I think Flamethrower would be a better choice. Yes, Weather Ball is stronger when it's sunny, but after that, Charizard will have no good STAB move, or no good damaging move at all for that matter, because Rock Slide *** sucks and should be replaced by Scorching Sands to hit Heatran and to actually do damage to Toxapex and Tyranitar.
Charizard-Mega-Y @ Charizardite Y
Ability: Blaze
EVs: 4 Def / 252 SpA / 252 Spe
Timid Nature
- Flamethrower
- Solar Beam
- Scorching Sands
- Roost
Greninja
Now, I'm not going to replace Protean Greninja (mainly because it synergizes poorly when paired with Mega Charizard Y), but that set is bad. It is pretty much a complete waste of a Z-move, and Water Shuriken and Grass Knot aren't good. There are many ways you can go with Protean Greninja.
Greninja @ Life Orb
Ability: Protean
EVs: 252 Atk / 4 SpA / 252 Spe
Hasty / Naive Nature
- Gunk Shot
- U-turn
- Ice Beam
- Spikes
Greninja @ Life Orb
Ability: Protean
EVs: 4 Atk / 252 SpA / 252 Spe
Hasty / Naive Nature
- Ice Beam
- Hidden Power [Fire]
- Gunk Shot / U-turn
- Spikes
Greninja @ Choice Scarf
Ability: Protean
EVs: 100 Atk / 156 SpA / 252 Spe
Hasty / Naive Nature
- Ice Beam
- Gunk Shot
- U-turn
- Hydro Pump
Serperior
Why are you using Miracle Seed with defensive EVs? Why use Miracle Seed and fully defensive EVs in the first place? Serperior is better off taking advantage of Leaf Storm's power and its utility options to be an offensive Substitute user.
Serperior @ Leftovers
Ability: Contrary
EVs: 56 HP / 200 SpA / 252 Spe
Timid Nature
- Leaf Storm
- Glare
- Substitute
- Hidden Power [Fire]
Gliscor
Normally, the set would be great, but unfortunately, due to your lack of hazard removal, this Gliscor needs Defog, which also means you should be using defensive Gliscor.
Gliscor @ Toxic Orb
Ability: Poison Heal
EVs: 244 HP / 56 Def / 188 SpD / 20 Spe
Impish Nature
- Earthquake
- Roost
- Defog
- Toxic / U-turn
Shuckle
You have Defog so Shuckle is pretty useless. I think that Toxapex would fit well here. More specifically, Specially Defensive Toxapex, which is rising to combat the uptick in Ash-Greninja usage. Ash-Greninja absolutely destroys your entire team, so you'd pretty much be hurting yourself by not using SpD Pex (or Blissey).
Toxapex @ Black Sludge
Ability: Regenerator
EVs: 252 HP / 4 Def / 252 SpD
Calm Nature
- Scald
- Recover
- Haze
- Toxic
