So, this team kind of looks like it pretty much loses to Kyogre and offensive Necrozma-DM, as well as lacking a good answer for Ho-Oh. You also have two Fairy-types which may be kind of unnecessary. I’m going to try to help with this.
Calyrex-Shadow
Draining Kiss is so weak without Dynamax and Life Orb. You should probably run Life Orb instead, as it provides an amazing power boost to your moves. Otherwise the set is fine.
Yveltal
Since you have another check to Calyrex-S in Ditto (if you decide to keep it), try 248 HP / 32 Atk / 228 SpD and Adamant in order to break its Sub with U-turn. Also consider minimum Speed with less Speed IVs to U-turn slower.
Xerneas
An alternative spread of 168 Def / 252 SpA / 88 Spe can be run in order to better live Necrozma-DM's hits while still outspeeding much of the metagame at +2. Substitute is also an option over Focus Miss; I mean, Blast, to better check Zygarde, which your team can struggle against. It also beats non-Power Whip Ferrothorn. An alternative spread of 44 HP / 124 Def / 252 SpA / 88 Spe can be used to make 101 HP Subs, which usually means beating Chansey and Blissey 1v1.
Zacian
Since you already have a Fairy-type setup sweeper in Xerneas, why not replace Zacian with a Kyogre check? In my opinion, Ferrothorn is best for this team. Sure, it loses to Ho-oh, but it has more utility than Eternatus. Xerneas and Calyrex-S appreciate the spikes it lays down, and you can even run Thunder Wave if you really want for better chances to setup. It also pseudo-checks Dragon Dance Necrozma-DM, which this team can fear a bit.
Ferrothorn @ Leftovers
Ability: Iron Barbs
EVs: 252 HP / 4 Def / 252 SpD
Careful Nature
- Power Whip
- Leech Seed
- Spikes
- Thunder Wave / Protect / Knock Off
I would recommend Thunder Wave for the last move as it can cripple many fast threats and neutralize Choice Scarf Kyogre, but Protect and Knock Off are also useful.
Necrozma-DM
Not much to say here, good set.
Ditto
So you mentioned this is kind of filler for this team. For this slot, you can run multiple things. Since this team now lacks a Physical sweeper, Zekrom can be great for dealing with Ho-Oh. Alternatively, Marshadow can also be used because it forms a nice attacking core with Calyrex-Shadow; as their checks can only handle so much. It also checks Ferrothorn which without Zacian, is hard to do (landing a Focus Miss does not count as reliably checking it XD)
Zekrom @ Lum Berry / Leftovers
Ability: Teravolt
EVs: 252 Atk / 4 SpD / 252 Spe
Jolly Nature
- Bolt Strike
- Dragon Dance
- Dragon Claw
- Roost / Substitute
Lum Berry if Roost to get a free Dragon Dance on Ho-Oh, but Substitute + Leftovers can also be used against more passive Pokemon and set up against them.
Marshadow @ Life Orb / Choice Band
Ability: Technician
EVs: 252 Atk / 4 SpD / 252 Spe
Jolly Nature
- Rock Tomb / Bulk Up
- Spectral Thief
- Close Combat
- Shadow Sneak
Life Orb if you don't want to be locked into one move, but Choice Band is also great for the much greater Power boost. Rock Tomb is great for beating Ho-Oh, and should always be run on Banded sets. For the Life Orb set, Bulk Up is an alternative to take advantage for the switches Marshadow forces, and it also gives this team a Physical setup sweeper. And before you yell at me in the comments that Poltergeist is better than Spectral Thief, look back at how many Knock Offs are on this team.
So that's my opinion on this team; any thoughts of my suggestions can be put below :P. Good luck playing Ubers, and I hope I helped!