I actually like gen 2 the most out of every generation. 3 is a close second for a lot of reasons but...
in my opinion, there's really something magical about generation 2. I love how it looks, it is on the perfect border of the right amount of detail for the sprites, the animations in crystal and stadium 2 are incredible, the colors of the shinies and the regular palettes are fantastic, i love kris, i love the way that the game is time based and how all the routes snake into themselves, i love how it is designed to be a long term experience kind of like a game of dungeons and dragons. I love how in gen 2 you have the game itself with Johto and then you have Kanto and THEN you have stadium...
Johto, to me, is still mysterious, it still feels like.. dark and edgy in a really fun way. And then theres part of Johto like the anime Johto that are warm and wholesome and feel like coming home in from the coldest storm and warming up from the inside out. And the movies.. oh the movies. The legendaries! My favorites, really in the whole series I think.
The merch too is phenomenal. I could look at gen 2 plushies all day long. Sighs dreamily.
I do love gen 3, I really do (hello, ribbons, I love you so much!!!) and I really have something that I really appreciate each generation for. Because, each generation is special in its own way and has something magic to offer you. And I kind of learn that more and more as I revisit, replay, reinvent how to play them... etc.
My only ?compliant? about gen 2 is that I am really, deeply sad about the battery clock save and how that wiped many save files with beloved pokemon. I also wish that the pokemon could cross the game to transfer over into generation three cartridges. Last I heard, there was someone working on the technology on their own to be able to accomplish this. I think they are still working on it and I would love to see it become a reality. Until then, I keep my Pokemon safely inside of Pokemon Stadium 2 whenever I take a break from spending time in Crystal.