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Mechanic Changes
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For any mechanic that's not described in here, assume Generation 9 mechanics.

Battle style is forced to set. 
Bag is inaccessible during trainer battles. 
Gym Trainers and Gym Leaders will heal your party to full before battle.
EVs are removed from the game.
TMs are consumed on use.
HMs do not need to be taught, obtaining them and having the required badge for use is enough.
Moves that are 1 PP for Player are 8 PP for AI (except Revival Blessing).

Critical hit chance for AI: 1/8 on Stage 0, 1/4 on Stage 1. 
Critical hit chance for Player: 1/16 on Stage 0, 1/8 on Stage 1. 
All remaining Stages are unchanged. These changes are not applied in Casual Mode.

Paralysis: Speed decreases by 75%.
Sleep: If a Pokémon enters a battle asleep it's sleeping turns count is reset.
Confusion: If inflicted by Berserk Gene, Self-Hit Power of 60 instead of 40.

Illuminate: Intimidate for Special Attack.
Leaf Guard, Magma Armor: Prevents critical hits on top of it's existing effects.
Battle Bond: Transforms Greninja into Ash-Greninja upon fainting a Pokémon.
Libero: Changes type every turn.
Tera Shift: Transforms into Stellar form if level 80 or above (AI only).

Terrain damage boost: Electric/Grass/Psychic Terrains will boost damage of moves of the matching type by 50%.
Terrain removal: Not removed by Defog or Ice Spinner.

Held items: Items that get consumed or removed from your Pokémon in any way during battle will not be restored.
Confuse inducing berries: Restore half HP, triggering at 1/4 HP.
Micle Berry: 1.5 Accuracy Boost instead of 1.2.

Safari Balls: 100% catch rate.

Berries cannot be planted.
No Pokémon take overworld damage from being poisoned.
Fishing always guaranteed to reel without precise timing.

Rotom Form Changing:
Birch's Lab now has appliances for Rotom.
Rotom-Wash will receive Surf over Hydro Pump.
Rotom-Frost will receive Ice Beam over Blizzard.
Rotom-Fan will receive Aeroblast over Air Slash.
When Rotom recalls into its base form, it's special Move will always be replaced with Shadow Ball.

IVs:
-Baby and Legendary Pokémon no longer have 3 IVs set to 31
-The Starter Pokémon and Type: Null have 3 IVs set to 31
-Traded Pokémon have 2 IVs set to 31

Level Cap:
Once a Pokémon reaches a level cap, the Common Candy item will no longer work and the Pokémon will not gain any experience. 
The level cap is tied to boss fights and raised as you defeat them. 
Here is a list of all the bosses and their matching level caps:

Root Academy Trainer 1     - Level 13
Root Academy Trainer 2     - Level 19
Root Academy Trainer 3     - Level 25
Root Academy Trainer 4 	   - Level 29
Leader Roxanne             - Level 38
Leader Brawly              - Level 45
Ex Elite Four Glacia       - Level 53
Leader Wattson             - Level 59
Leader Norman              - Level 66
Leader Flannery            - Level 72
Leader Winona              - Level 77
Magma Hideout Maxie        - Level 82
Leader Tate & Liza         - Level 86
Seafloor Cavern Archie     - Level 91
Leader Steven              - Level 95
Ex Elite Four Glacia 2     - Level 99
Champion Wallace           - Level 100