Here is a list of games I'd recommend checking out
Fan Games
Pokemon Reborn - (Love the story, soundtrack, characters and challenging AI) 10/10 Pokemon Rejuvenation - (Love the story, soundtrack, characters and challenging AI) 10/10 Pokemon Desolation - In similar vein to Reborn and Rejuvenation. Excellent Game! Still currently playing Pokemon Empyrean - Haven't finished but is an awesome game so far. Different feel to the previous three yet fun. Pokemon Insurgence - This is a fun game. New Megas and Deltas look great! Only complaint is misplaced soundtrack or lack there of. Story is okay Pokemon Sage - Incomplete but the best design Fakemon I have ever seen Pokemon Uranium - Haven't finished yet. But it is pretty good so far. It's a Fakemon game that follows traditional Pokemon formula Pokemon Spork - I haven't played this one in a while but a lot of optimization from what I remember
Rom Hacks (with Original story)
Pokemon Gaia - Very well made game. Brand new region yet it feels like an official Pokemon game
Pokemon Glazed or Blazed Glazed - Original Tunod Region. Includes Johto as well. Well made game indeed.
Pokemon Adventure Red - Follows the Pokemon Manga if you are into that. Very fun game
Pokemon Dark Violet - (Best Fire Red Remake in terms of Updated Story)
Pokemon Ruby Destiny: Life of Guardian - Still currently playing this and so far it is good. Multiple endings I've heard. Soundtrack is good
Pokemon Prism - If you like Retro GBC style, you will love this game! Lots of Customization , Original Region and fun story
Pokemon Grape - Also Retro GBC style but Red & Blue style instead of Crystal. Brand New Region! The story is confusing but fun play through nonetheless
Rom Hacks that are essentially remakes
Pokemon Radical Red - Includes up to Gen 8! (Best Mechanics and Increased Difficulty)
Pokemon Sacred Gold & Storm Silver - Remake of Heart Gold and Soul Silver. More variety and increased difficulty
Pokemon Blaze Black & Volt White - Remake of Black & White. More variety and increased difficulty
Pokemon Blaze Black 2 & Volt White 2 - Remake of Black 2 & White 2. More variety and increased difficulty
Pokemon Renegade Platinum - Remake of Platinum. More variety and increased difficulty
Pokemon GS Chronicles - Updated Gen 2 Johto Region but using the Gen 3 Games
Pokemon Crystal Clear - Basically Open world Version of Pokemon Crystal GBC Style. You can battle Gym Leaders in any order and the AI levels scale depending on badges