There are probably more differences from vanilla mechanics that I haven’t realized. Please tell me if you find one.
Sachet
In vanilla Pokémon, Sachet only evolves Spritzee. In YAPU, Sachet also boosts Fairy moves, to complete the Type-Enhancing items cycle.
Gems
Gems boost moves by 50% instead of the 20% of modern games.
Repels
Max Repel lasts for 300 steps instead of 250, making it actually better value than the Super Repel.
Red Card
In vanilla Pokémon, if a wild Pokémon in a single battle is holding a red card, is hit by the player and the player only one has one Pokémon in their rooster, the red card will not trigger the player running away. In YAPU, it will trigger the running away regardless of the number of Pokémon in the roster.
Eject Button
In vanilla Pokémon, if multiple Pokémon holding an eject button are hit by the same attack, only the fastest will trigger their Eject Button. In YAPU, all of them will trigger.
Everstone
In vanilla Pokémon, the Everstone prevents any Pokémon from evolving except for Kadabra. That weird exception doesn’t exist in YAPU. It will also prevent Pokémon from evolving with evolution stones or similar.
Lucky Punch
Lucky Punch also affects Happiny and Blissey.
Sacred Ash
Sacred Ash completely heals the party instead of only restoring HP because it’s cooler this way.