As everybody says Drayano hacks, my personal favorite is Pokémon Prism by Koolboyman. I originally found this hack back in 2011 when it was a 4-gym beta and I loved all the new mechanics added such as new types (before fairy godparents existed) that balanced the entire dex, added future necessities such as futuremons, a physical/special split, and even some mystery dungeon action, all in gen 2. This hack was the hack that initially brought me back into Pokémon after dropping the franchise in 2004, when gen 3 abandoned the Game Boy Color, when my friend (allegedly) stole Pokémon Crystal another friend gifted to me, the anime was moved to cable, and I gave my cousin all of my trading cards from Base Set 2 to Neo Genesis (regretting that now). I kept up with the hack development through the years and played the demo (which is archived on the old site in Completed Adventures) back in 2015. And then in 2016, it was announced that under a renovation using Crystal as its base, the complete version would be released on Christmas after the Twitch Plays Pokémon run of it. Alas, because of Pokémon Sun and Moon, the publicity caught the eye of Nintendo, and they sent a cease and desist to Koolboyman and all of the staff working on this game. The file still exists in 4chan somewhere and a smaller team came in and polished all the bugs from the twitch build in patches. Nowadays, the hack as it is has grown bigger: it now includes the Fairy type in place of another type, abilities have been added as well as natures and characteristics, brand new demade music, and there is even a more robust customization than the vanilla games, plus more. There aren't that many hacks that utilize the game boy era, but this is the best one. Note: you might have to play Brown version (a hack of Red) to get some idea of Prism lore, but it is entirely optional.
As for a minor slice of life hack, Crystal Clear is a masterpiece. New music that can be selected from nearly all generations (/some not from Pokémon), a built in soft reset system for shiny hunting, which has been increased x4, your Pokémon being able to follow you (and can be chosen from any of the 6 slots instead of just the top), and best of all, the entire game is open world. You're free to tackle any gym in any order since HMs are no longer badge-locked and trainers scale to your levels with gym leaders having an appropriate team depending on what stage you're fighting them. After defeating a gym leader and gain more badges, you can rematch them anytime by number of badges and each level has a different team appropriate to that level. Also, I believe certain areas have been restored, but don't take my word for it. Again, this is another hack you have to search for because the creator in fear of nintendo shutting it down from the amount of publicity gained has mostly removed it from his site.
But Poopawman, I don't like Crystal! Is there a hack that uses Fire Red or Emerald as a base? (Damn, so much for liquid crystal, the long lost remake to hg/ss) OK, for you gen three-ers, I have two: For lovers of the anime, there is Ash Gray, which closely follow the events of the original series and the Orange Islands, and for the edgelords that read the manga, Red Adventures follow the manga plot but also add minor filler that add color to a fledged-out story. I don't know how far the reboot hack is up to now, but the original Adventures hack go up to the Orange Islands as well. As for Ash Gray, last I played, I remember a bug that needed walk through walls to advance the story because a gate caused the game to crash.
There, 4 (5 if you want to check out Liquid Crystal) recommendations for good hacks that are not Drayano.
