Preferably one that's not a rom hack, though I dig those too. I'm looking for something a bit harder than the originals and maybe a bit more mature, but still fair and whimsical. I'd like a game with pokemon from as many gens as possible, and fakemons are fine too.
I know you said you’re looking for something harder and more mature, but I cant help but recommend Pokémon Bushido, and Pokémon Xenoverse. Both excellent games imo.
If you want something familiar but also completely different, go with Pokemon Emerald Rogue. It does what it sounds like and turns the game into a roguelike.
Pokemon Theta Emerald Renev is one of my favourites. It's basically Emerald, but with updated mechanics, attacks, and Pokemon, so you can have up to Gen 7 Pokemon in your team. The Pokemon list also means you can complete the Pokedex mostly on your own, and other cool features. Definitely recommend checking it out.