More and more, lately, I find myself returning to Gen 2 over everything else. There's nothing else like it, even within the series. Even the brilliant remakes in the form of HGSS aren't quite the same (but they’re very high on my list as well). Crystal is probably my favorite as a result. I have my little nitpicks, like how I appreciate how Gold and Silver make the opposing box legend level 70 instead of the 60 that they're both at in Crystal, or how I think that there's something beautiful in the subtle simplicities that Gold and Silver have over Crystal - but regardless, the Gen 2 games as a whole remain the best experience for me.
Beyond that, honestly, the next best thing this series has to offer is Legends. I had more fun playing Legends than I had with anything else since I first picked up Silver over 2 decades ago, and I think it should be the foundation of the future of the series. It's the first step in the right direction and I'm excited that Scarlet and Violet seem to be taking some notes from it stylistically.
Third is Hoenn - Emerald, specifically, the perfect embodiment of the sense of endless wonder and adventure from that beautiful region. The Battle Frontier helps it stand above Ruby and Sapphire, among other things. I think it's another near-perfect implementation of the Pokemon vision, just in a different direction from the other two I mentioned.
I love the series, and there are a lot more games I didn’t even mention that are probably worth mentioning, but those are my absolute favorites.