Time to rate a team.
Finally, Natdex Ubers, a metagame I know.
Let's start off with a general overview of the team. As you helpfully noted, you have a lot of physical attackers, and a big Ice weakness. These are also problems that my team had for a while. (and the problem persists somewhat.) I've found that many physical attackers isn't a huge problem, you just need to focus on a way to deal with Will-O-Wisp users (Read: Giratina and Arceus) and Physical Walls. (Arceus, Dondozo, and Groudon-P)
The Ice weakness isn't a huge problem, the most common Ice-type attackers are Kyurem White and Black and Mega Mewtwo Y. Chien-pao and Baxcalibur are rare, and Calyrex-Ice needs Trick Room to do anything. Iron Bundel is a threat, but it's power is kind of bad without the super effective multiplier, Groudon-P should work well against many of the good Ice users, and Necrozma-DM can do well if you don't Ultra Burst.
Now let's get to the actual team itself: (Although there probably won't be much to say. It looks pretty good.)
Deoxys-S
Psycho Boost over Spikes is the only change I would make. Looks fine.
Salamence-Mega
The set looks fine. Something you can try is using Moxie as the base ability, because it allows you to finish a slower target off with base form Salamence, and get +1 Attack before Mega Evolving. Intimidate works well too though. You may want Double Edge over Frustration, because...
Rayquaza
This set needed an Ice weakness removed, and removing a physical attacker would be good as well. I know Raquaza is part of the core, but I think he should be cut. Mega Salamence is a little better, and two 4x Ice weaknesses don't go well together. Groudon-P can still do a great job checking threats to Salamence. A Special attacker would be good to slot in here instead. Here are some options:
Kyurem-White @ Choice Scarf
Ability: Turboblaze
Tera Type: Fire
EVs: 84 HP / 252 SpA / 172 Spe
Timid Nature
IVs: 0 Atk
- Draco Meteor
- Freeze-Dry
- Fusion Flare
- Ice Beam
Here is the White Kyurem set that I use. It acts as speed control (Outspeeds All unboosted but Regieleki, Deoxys-S and Ninjask) It can OHKO Zacian Crowned with Tera Fire Fusion Flare (252 SpA Tera Fire Kyurem-White Fusion Flare vs. 0 HP / 4 SpD Zacian-Crowned: 356-420 (109.5 - 129.2%) -- guaranteed OHKO)
This thing destroys most dragons in the Uber Tier.
Koriadon, (252 SpA Kyurem-White Ice Beam vs. 0 HP / 0 SpD Koraidon: 360-426 (105.5 - 124.9%) -- guaranteed OHKO)
And Eternatus (252 SpA Kyurem-White Draco Meteor vs. 0 HP / 4 SpD Eternatus: 542-638 (128.7 - 151.5%) -- guaranteed OHKO)
Even the bulkiest Coil Zygarde is no longer a problem: (252 SpA Kyurem-White Ice Beam vs. 252 HP / 252+ SpD Zygarde: 540-636 (128.5 - 151.4%) -- guaranteed OHKO) (Technically, Zygarde survives with max HP, SpD and an Assault Vest, but who on earth uses Assault Vest Zygarde?)
You could also use Kyogre, Primal or Scarf. Specs or Life Orb Mewtwo works well too.
Groudon-Primal
Looks fine. Stone Edge is usually a better choice than Heat Crash, but on this team, it works. Try to keep Groudon alive, as he's a VERY important part of this team.
Yveltal
Also looks fine. Heat Wave?
Necrozma-DM
I use Sunsteel Strike over Stone Edge, to deal with Faries, and it gets STAB in Duck Mane Form. If you want to use Zacian over this guy, you could. I recommend testing the team with Zacian, and without.
So far, I have addressed everything on your list of concerns, except for Arceus-Dark, who is a real pain. Yveltal can win a 1v1 with it, but most players won't let you Oblivion Wing them to death. The White Kyurem set I gave does well too.
Mewtwo OHKOs with Aura Sphere after a Nasty Plot: (+2 252 SpA Life Orb Mewtwo Aura Sphere vs. 248 HP / 0 SpD Arceus-Dark: 442-520 (99.7 - 117.3%) -- 93.8% chance to OHKO)
So does Scarf Kyogre: (252 SpA Tera Water Kyogre Water Spout (150 BP) vs. 248 HP / 0 SpD Arceus-Dark in Rain: 468-552 (105.6 - 124.6%) -- guaranteed OHKO)
With a team that's already so good, this is the best advice I can give you. Hope I helped. Have fun, and beware the webs Smeargle. (Possibly the most annoying type of team in Ubers.)