Ok, so I am going to be honest — this team probably won't last at all in an actual tournament.
First off you are countered hard by Primal Groudon and Mega Rayquaza, as they won't let get off any rain, hindering your whole team. Second your team is really weak to being setup on by Trick Room/Tailwind setters, and Geomancy from Xerneas.
With all this in mind, I am going to tell you how to fix it.
First off you gotta drop out Chesnaught. I know you said it has to be ther, but it is the only thing keeping the team behind. It is crazy unusable in VGC. From what I can tell you are trying to make it something that will prevent you from being set up on by Xerneas, as it has Roar. It will be destroyed by Rayquaza, Incineroar, Groudon, Xerneas, Yveltal, Tapu Koko, etc. Replace it with Amoongus
Replacement 1: Chesnaught --> Amoongus
Amoonguss @ Focus Sash/Wiki Berry
EVs: 252 HP / 100 Def / 156 SpD
IVs: 0 Atk
- Rage Powder
- Clear Smog
Protect is a staple move it VGC as it allows you to scout through your opponents moves. Spore allows you to threaten a lot of mons, although Electric Terrain and Misty Terrain will prevent it from putting a foe to sleep. Clear Smog allows you to prevent being setup on Amoongus. Rage Powder + Focus Sash will provide support for he next mon that will be added to your team...
Replacement 2: Sylveon --> Xerneas
Xerneas @ Power Herb
Ability: Fairy Aura
EVs: 44 HP / 20 Def / 188 SpA / 4 SpD / 252 Spe
IVs: 0 Atk
- Dazzling Gleam
Xerneas does Sylveons job but better. With Geomancy it will end doing crazy damage to a lot of teams, making it very hard to counter. Dazzling Gleam, since this is doubles, Protect, since this is VGC, Geomancy, as it doubles Speed, Special Defense, and Special Attack, and finally Moonblast for dealing extra powerful damage. If Amoongus and Xerneas are both on the field, Amoongus can use Rage Powder for a guaranteed chance of Xerneas getting off a Geomancy.
Replacement 3: Dragonite --> Incineroar
Incineroar @ Assault Vest
EVs: 252 HP / 196 Atk / 60 SpD
- Fake Out
- Flare Blitz
- Knock Off
Dragonite had good intentions, but is countered way to har by the most comon Pokemon in VGC, such as Incineroar, Xerneas, Fini, Koko, Kyogre, etc. Incineroar is something your team needs. A lot of your team is countered pretty hard by most physical attackers. With intimidate Incineroar can force switches and pressure physical attackers. Fake Out provides additional pressure to almost all Pokemon, excluding ghost types. U-Turn can allow Incineroar to easily apply even more intimidate pressure. Knock Off to remove items which may be helpful to your opponent. Flare Blitz is just powerful in general.
Replacement 3: Aegislash --> Kyogre
Kyogre-Primal @ Blue Orb
Ability: Primordial Sea
EVs: 204 HP / 156 Def / 76 SpA / 4 SpD / 68 Spe
IVs: 0 Atk
- Water Spout /Origin Pulse
- Ice Beam /Icy Wind
- Origin Pulse/Thunder
Primordial Sea allows for rain to be up, until Kyogre is switched out, knocked out, or when M-Rayquaza or Groudon-Primal come on the field. Protect, since this is VGC, Water Spout has a base power of 150, but its power decreases as Kyogres health decreases. Ice Beam and Icy Wind are for mainly Rayquaza and Salamance, and you can choose either one of those for your Kyogre. Origin Pulse is a very powerful move, and can be used when Kyogre has low health, but Thunder can be used to hit other Kyogres and flying types.
Final Replacement: Naganadel --> Tapu Koko
Tornadus (M) @ Electrium-Z
EVs: 4 HP / 252 SpA / 252 Spe
IVs: 0 Atk
- Natures Madness
- Dazzling Gleam
Naganadel is countered to hard by Groudon, Kyogre, and Xerneas(after Geomancy). If you did really want to run Naganadel, replace Nasty Plot with Protect, and give it Posinium-Z, as it probably wont live enough hits for black sludge to be helpful. Thunder does not miss in rain, Natures Madness allows you to take a lot of damage on your opponets Pokemon, allowing them to be more easily KOed. Dazzling Gleam hits both foes, and Protect allows move scouting.
Adujustments to Mega Swampert:
Swampert-Mega @ Swampertite
Ability: Swift Swim
EVs: 4 HP / 252 Atk / 252 Spe
- Ice Punch
With your previous set, Swampert will still be outsped by Tapu Koko during rain, so Tapu Koko could still deal bad damage to Kyogre before being taken out. Swamperts Tankyness will still allow it to live through multiple, even with only 4 HP. Ice Punch for Rayquaza and Salamance and other flying types, Earthquake is powerful, but will also hit Swamperts ally so be careful of that. Waterfall is for stab, and it hits a lot of other mons pretty hard.
I hope these tips improve your team and you can win a tournament or something :)
Also Groudon is still a pretty big threat to your team, but Kyogre and Xerneas are in the top ten Pokemon who defeat Groudon , and you can probably easily work around it anyway, with Initmidate Incineroar, Natures Madness on Tapu Koko, etc.