Even with a +Defense nature, Dialga is still wrecked by powerful Fighting/Ground moves. Heck, it's still wrecked by (Primal) Groudon:
252+ Atk Primal Groudon Precipice Blades vs. 252 HP / 252+ Def Dialga: 350-414 (86.6 - 102.4%) -- 18.8% chance to OHKO
Anyway, Primal Groudon is seriously good; it's incredibly versatile and it can check opposing Xerneas somewhat better, even though it doesn't normally carry moves that hit it super effectively. In the OR/AS shift, Primal Groudon took many niches that its fellow Ubers held, including Dialga's:
-Stealth Rock
-Earthquake/Precipice Blades
-Lava Plume/Stone Edge
-Roar/Thunder Wave
Nature: Relaxed
EVs: 252 HP/56 Def/200 SDef
Item: Red Orb
or
-Stealth Rock
-Precipice Blades
-Dragon Tail/Stone Edge
-Fire Punch/Stone Edge
Nature: Adamant
EVs: 224 HP/240 Atk/32 SDef/12 Spe
Item: Red Orb
Chansey's Special Attack is incredibly wimpy, meaning that it's forced to use Seismic Toss for consistent damage and Ice Beam is incredibly weak coming off of it; it doesn't even 2HKO Rayquaza for instance. Chansey has to rely on Toxic and Seismic Toss for its damage:
0 SpA Chansey Ice Beam vs. 0 HP / 4 SpD Rayquaza: 128-152 (36.4 - 43.3%) -- guaranteed 3HKO
Even if this suggestion means losing out on cleric utility, Defog Arceus isn't a bad option to consider:
-Judgment
-Defog
-Will-o-Wisp
-Recover
Nature: Timid
EVs: 248 HP/8 Def/252 Spe
Item: Spooky Plate
With Xerneas and Fairy Arceus being rather prominent threats in Ubers, it's risky to have Mega Salamence use Outrage this gen. Besides, it has Aerilate Return/Double-Edge as its source of raw power already; it outdamages Outrage:
-Dragon Dance
-Return/Double-Edge
-Earthquake/Substitute/Refresh
-Roost
Nature: Jolly
EVs: 252 Atk/4 Def/252 Spe
Item: Salamencite
Ability: Intimidate
or
-Dragon Dance
-Return
-Refresh
-Roost
Nature: Impish
EVs: 248 HP/136 Def/124 Spe
Item: Salamencite
Ability: Intimidate
Lugia's Speed is naturally high for a wall. IMO, it should focus on its bulk rather than its Speed:
-Roost
-Toxic
-Whirlwind/Dragon Tail
-Reflect/Aeroblast/Thunder Wave/Substitute
Nature: Bold/Impish
EVs: 252 HP/120 Def/136 Spe
Item: Leftovers
Thanks for the suggestions! Do you feel Kyogre is okay/still fits on the team after the changes? I decided to swap out Dialga for Primal Groudon because Dialga was definitely my biggest weak spot. I went for the bulkier more support set since I felt the tankiness would help more here.
Team after the changes:

Kyogre @ Blue Orb
Ability: Drizzle
EVs: 248 HP / 252 SpA / 8 Spe
Modest Nature
- Origin Pulse
- Ice Beam
- Thunder
- Calm Mind

Lugia @ Leftovers
Ability: Multiscale
EVs: 252 HP / 120 Def / 136 Spe
Bold Nature
- Toxic
- Roost
- Whirlwind
- Aeroblast

Salamence @ Salamencite
Ability: Intimidate
EVs: 252 Atk / 4 Def / 252 Spe
Jolly Nature
- Return
- Roost
- Dragon Dance
- Earthquake

Xerneas @ Power Herb
Ability: Fairy Aura
EVs: 252 SpA / 4 SpD / 252 Spe
Modest Nature
- Geomancy
- Moonblast
- Thunder
- Focus Blast
Groudon @ Red Orb
Ability: Desolate Land
EVs: 252 HP/56 Def/200 SDef
Relaxed Nature
-Stealth Rock
-Precipice Blades
-Stone Edge
-Thunder Wave

Arceus @ Spooky Plate
Ability: Multitype
EVs: 248 HP/8 Def/252 Spe
Timid Nature
-Judgment
-Defog
-Will-o-Wisp
-Recover
@ArmourPearlShipper
I decided to drop both Chansey and Dialga for now to see how these changes work, but if I see I miss Chansey too much; I'll try out Blissey. I have just always preferred Eviolite Chansey but I do realize that makes me knock off bait.
I did decide to make the Kyogre EV changes though. Thanks!