I think including past gimmicks - like Mega Evolution and Z-moves - but not pointing them out to the player might be cool. That way the player is rewarded for exploring this cave with a Normalium-Z or something to make future fights easier. Between the two there's about 85 of these items in canon, and there's no reason there can't be more exclusive Z-Crystals / Mega Evolutions if you can think of some. It'd help make more Pokémon feel more equal to each other, since all Pokémon are available in this game concept, and it would make the world have more stuff in it and seem fuller. Plus, you can sell the game as having all of the last three gens' major gimmicks (or at least the two from the 3DS era).
I also recommend that while most areas have levels based on the player's, maybe make it so that the levels of Pokémon are slightly lower / slightly higher than the party's in certain areas? This would be a good thing in tandem with the first idea to make it so that said cave with a secret item in it seems more like a challenge, to make the Z-crystal more rewarding. (Since the player can have 6 pokemon, and wild pokemon are in parties of one, having slightly higher level Pokemon than the party's in these areas isn't actually a bad thing.)