There are probably more differences from vanilla mechanics that I haven’t realized. Please tell me if you find one.
Compound eyes and Super Luck
Compound eyes and Super luck have no effect out of battle, like in gen IX.
Unnerve
Unnerve affects all callbacks that check if the battler can use its held item. This means it affects callbacks that don’t involve eating like choice items or items that modify power like plates. This doesn’t change the behaviour of vanilla berries (since none of them have those effects) but it something to take into account if game devs wanted to implement a choice berry, for example.
Lightning Rod
Lightning rod properly attracts moves that calculate their type dynamically like Judgement or Hidden Power.
Slush Rush
Unlike in vanilla, Slush Rush prevents from being damaged by hail, like its counterpart Sand Rush. This doesn’t affect currently existing Pokémon.
Sheer Force
Sheer force doesn’t affect the effects of objects or abilities, only the secondary effects of moves.
Cute Charm
Cute Charm has no effect out of battle, like in gen IX.
Stench
Stench does stack with King’s Rock and similar effects.
Arena Trap
If a Pokémon decided to switch out or flee at the beginning of the turn and a Pokémon with Arena Trap switches in, they will no longer be able to switch out.
Flame Body, Magma Armor and Steam Engine
Instead of having the egg cycles required for each egg, these abilities half the steps required for each cycle, resulting in the same effect. They also stack with each other.
Own Tempo
The Pokémon will get confused, but will be inmediatly cured.
Imposter
Check Transform.
Forecast
A transformed Pokémon can switch forms with Forecast, just like before gen V. A Pokémon with Forecast that has it suppressed will stay in its current form, just like before gen V.
Protean
Protean trigger every move, like before gen IX.