I'm no good at Nat Dex AG, so take this with a pinch of salt :)
Calyrex-Shadow
- Fairium Z < Ghostium Z/Buginium Z. This is because Twinkle Tackle has same BP has Max Starfall. Hence, it's not a good choice since you lose Dynamax at the cost of a 100 BP move. Plus, it doesn't OHKO many things compared to Ghostium or Buginium.
Against Arceus-Dark:
+2 252 SpA Calyrex-Shadow Twinkle Tackle (100 BP) vs. 252 HP / 132+ SpD Arceus-Dark: 362-428 (81.5 - 96.3%) -- guaranteed 2HKO
Against Tyranitar:
+2 252 SpA Calyrex-Shadow Twinkle Tackle (100 BP) vs. 252 HP / 252+ SpD Tyranitar in Sand: 250-296 (61.8 - 73.2%) -- guaranteed 2HKO after Leftovers recovery
Now let's look at Buginium Z.
+2 252 SpA Calyrex-Shadow Savage Spin-Out (175 BP) vs. 252 HP / 252+ SpD Tyranitar in Sand: 438-516 (108.4 - 127.7%) -- guaranteed OHKO
+2 252 SpA Calyrex-Shadow Savage Spin-Out (175 BP) vs. 252 HP / 132+ SpD Arceus-Dark: 634-748 (142.7 - 168.4%) -- guaranteed OHKO
This makes it much more effective than Fairium. So get rid of that and get a Buginium Crystal.
Necrozma-Dusk-Mane
- Serious Nature < Adamant/Jolly Nature. Well that's all. You don't really need Photon Geyser—Stone Edge is much more better. It allows you to beat Ho-Oh in one hit and Yveltal after Weakness Policy boost.
- Go for Defensive set. Explained why later.
Necrozma-Dusk-Mane @ Rocky Helmet
Ability: Prism Armor
EVs: 252 HP / 252 Def / 4 SpD
Impish Nature
- Sunsteel Strike
- Morning Sun
- Stealth Rock
- Knock Off
It's a better Stealth Rock setter than Tyranitar which also helps to beat Xerneas.
Lugia --> Ho-Oh
- Lugia isn't better than Ho-Oh/Yveltal. This team has no Defog, now time for Sticky Web and Stealth Rocks to give your team a painful death. Ho-Oh is good Defogger, but Yveltal's a good bet right now. Your team has horribly bad MU against Calyrex-Shadow, so I suggest getting a Yveltal. Also, replace Autotomize Necrozma-Dusk-Mane with Defensive Necrozma-Dusk-Mane to get a better match-up against Zacian-C.
Yveltal @ Heavy-Duty Boots
Ability: Dark Aura
EVs: 248 HP / 8 Def / 252 SpD
Careful Nature
- Foul Play
- U-turn
- Defog
- Roost
Zygarde
- What's up with that weird set? You had wanted to go fully Defensive else Primal Groudon wipes your team. Sp.Def on it is weird and unconventional. The Atk EVs on it doesn't matter, since Coil is preferred on fatter teams, not fast ones. Also, Rest > Dragon Tail so that you can switch-in more consistently to Primal Groudon plus to wave off status.
Zygarde @ Leftovers
Ability: Power Construct
EVs: 252 HP / 252 Def / 4 SpD
Impish Nature
- Coil
- Glare
- Thousand Arrows
- Rest
Tyranitar --> Primal Groudon
- Since we already have Yveltal, get rid of Tyranitar. It's main problem is due to those crazy Baton Pass and Savage Spin-Out crawling the ladder, it doesn't get much more importance right now. Instead, get a good Primal Kyogre counter. It is capable of sweeping this team. Best is our Primal Groudon right now :)
Groudon @ Red Orb
Ability: Drought
EVs: 252 HP / 36 Def / 220 SpD
Sassy Nature
Xerneas
- Looks neat to me. Nothing needed to improve.
Final team
Hope I helped!
