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Besides the ones mentioned at OP, I'd remove redundant objects like Plates and Memories and replace them with Z-Stones and/or the generic type-boosting items (Silk Scarf, NeverMelt Ice, etc.)
Some adjustments in movesets and stat boosts to regular Pokémon. New abilities for every species and revamp the breeding system (to make it easier to choose the ability.)
Remove Shedinja's Defense and Special Defense points, leaving it with only 1 in both.
Lower the burning chance of Scald to 10 %, and up the chance of Flamethrower to 20 %. Lower U-Turn's and Knock-Off's damage to 40. Stealth Rock can now be removed by Rock-Type Pokémon on switch. Fairy type is now weak to Bug (or at least doesn't resist it) and resisted by Grass/Ice. Hail now lowers the defenses of non-Ice type Pokémon by 10 %. Sunny Day ups the probability of burning an opponent with a Fire-type move by 10 %. Sound-based moves do critical damage (or apply their effects x2 in case of moves such as Growl) to targets behind Substitute. Thunder, Blizzard and Hurricane have a 20 % chance of hitting targets behind Protect. Silvally gets +5 on all stats. New natures can now affect the HP stat. The Pokédex now has entries for learnset of moves (and how they're learned), egg group, species found in each area, evolution methods and catch ratio; a new ability that sets Trick Room when the Pokémon is sent and a new item that boosts Trick Room from 5 turns to 8.
That's about all I could think off the top of my head.
