Your team is fine. Some things you should consider:
Putting more pressure into Defoggers
Yveltal @ Heavy-Duty Boots
Ability: Dark Aura
EVs: 252 HP / 4 Def / 252 SpD
Careful Nature
IVs: 28 Spe
- Foul Play
- U-turn
- Defog
- Roost
This Pokemon, and this set seems to be be problematic for the team. Paired with Ditto, it doesn't seem to be easy to handle, especially it can disable Calyrex-Shadow's Focus Sash with U-Turn, then go into Ditto which just outspeeds. To better handle it, you can have a different Yveltal set. The option is to have Taunt replace Sucker Punch or use a Physical Hone Claws set which is extremely destructive!!
Yveltal @ Life Orb
Ability: Dark Aura
EVs: 252 SpA / 4 SpD / 252 Spe
Timid Nature
IVs: 0 Atk
- Dark Pulse
- Oblivion Wing
- Heat Wave
- Taunt
Alternatively, a physical Hone Claws Yveltal can tear through teams like a breeze.
Yveltal @ Life Orb
Ability: Dark Aura
EVs: 252 Atk / 4 SpD / 252 Spe
Adamant Nature
- Knock Off
- Dual Wingbeat
- Sucker Punch
- Hone Claws
What's scary about Physical Yveltal that it has very limited checks. It can easily break through standard NDM + Etern + Yve cores while OHKOing almost everything Dynamaxed after a Hone Claws boost. Can give calculations to prove it, as well:
+1 252+ Atk Life Orb Dark Aura Yveltal Knock Off (97.5 BP) vs. 252 HP / 252+ Def Prism Armor Necrozma-Dusk-Mane: 417-493 (104.7 - 123.8%) -- guaranteed OHKO
+1 252+ Atk Life Orb Yveltal Max Airstream vs. 252 HP / 4 Def Yveltal: 476-562 (104.3 - 123.2%) -- guaranteed OHKO
+1 252+ Atk Life Orb Yveltal Max Airstream vs. 240 HP / 0 Def Eternatus: 477-563 (99.1 - 117%) -- 93.8% chance to OHKO
Impostor proofing better
Ditto @ Choice Scarf
Ability: Imposter
EVs: 248 HP / 8 Atk / 252 Def
Relaxed Nature
IVs: 0 Spe
- Transform
The thing that comes into mind the most while building HO after suicide leads is this. Improofing so that Choice Scarf Ditto doesn't ruin your day.
Currently, this team has Necrozma-DM and Calyrex-Shadow checked by your own Yveltal and Calyrex-S. However, Kyogre and Yveltal haven't been sufficiently improofed. If Ditto transforms into one of them, then it's actually hard to play around. The solution is to have a Eternatus or a niche pick like Palkia that can improof Kyogre, or another choice is to replace Kyogre. While as much as I love using Specs Kyogre in Webs, its not good if you don't improof it better. For that, I suggest using Xerneas as its checked on its own by Necro DM. It can also handle Yveltal, so not a bad choice at all.
Kyogre --> Xerneas
Xerneas @ Power Herb
Ability: Fairy Aura
EVs: 44 HP / 252 SpA / 212 Spe
Modest Nature
- Geomancy
- Moonblast
- Thunder
- Substitute
The sweeping deer! Any more explanation needed? Since we're having physical Yveltal as our Dynamaxer, having a Special Dynamaxer is also good. 44 HP allows you to create 101 HP Substitutes, which means Chan-sis require 2 Seismic Toss to break one Sub. Rest are on SpA for power, and Spe to ensure you outspeed things, as the bulk isn't needed much.
Caly-S set need to be changed
Focus Sash with Draining Kiss is bad. You can't OHKO SpD Yveltal with a +2 Max Starfall. Even though, I had not suggest removing the Focus Sash. Instead of Draining Kiss, why not something like Baton Pass? A +2 to Xerneas is nearly impossible to wall, so it's not a bad choice to use that instead. Also, on second thoughts use Taunt instead of Psyshock. Taunt makes Chansey bait as it can't Toxic you, but importantly prevents Yveltal from Defogging your Webs. It might be a bit of a risk, but it's actually worth it, imo.
Calyrex-Shadow @ Focus Sash
Ability: As One (Spectrier)
EVs: 252 SpA / 4 SpD / 252 Spe
Timid Nature
IVs: 0 Atk
- Nasty Plot
- Astral Barrage
- Taunt
- Baton Pass
Rest of the team is solid in my eyes. Hope my suggestions helped you!
Updated Team