Perfect Crystal or Crystal 251 sound like what you're looking for- mostly vanilla with bugs fixed.
I'll go ahead and throw out a rec for Polished Crystal also, because it's my favorite gen 2 hack and I just think it's neat. The PokeCommunity files are out of date, but there's steady updates through the dev's discord & GitHub.
Could also build your own copy from pokecrystal I guess- they have documentation for fixing the bugs in the code. But that's definitely not low effort, lol.
My nostalgia goggles tinting things a bit here, but Gen 2 (GSC) felt like such a jump in quality compared to RBY; especially Crystal.
- Moved to full color
- Animated sprites
- Character selection
- RTC & the day-night cycle
- Both regions & 16 badges
- QOL mechanics (hold items, eggs/breeding, A to use HM, rematches, Mom bank, Move Deleter)
- Dark & Steel type additions
Johto gets a lot of flak for the level curve, but the game just felt so big at the time, seems like that should count for something. Also I just like its vibe.
I don't think any other gens have felt like such a complete step up compared to previous ones for me. B&W came closest, probably, was bummed they didn't keep seasons. Made the world feel more dynamic. The 3D stuff is fine, just feels more wooden. They lost a lot of the charm moving away from pixel art.
I really love the remixed themes in Pokemon Puzzle Challenge. The title opener is a bop also.