Favorite:
Crystal (G/S were awesome as well, but I choose Crystal because it finally stopped forcing me to be a male trainer, and it was also the third in line, which are the best).
I pretty much liked everything about it... I really had a blast playing through it and I'm not talking about nostalgia here, I clearly remember thinking it was the best back then as well lol.
I liked the addition of the day and night system, as well as the weekdays system as well. I liked the sense of realism, and also the events and Pokemon that you could only catch at certain times. I liked that you could rebattle trainers. All in all it gave a feeling of "This game is endless", and the game also felt complete. The amount of Pokemon that I could catch was great. And going to Kanto and getting another eight badges and seeing how it had changed over the last three years, it was amazing!
Least Favorite:
Ruby. As opposed to Crystal, this game felt incomplete. I don't dislike it or anything, it just was ultimately disappointing having come from playing Crystal.
It just felt so limiting. The game was fun to play through a couple of times, but as for replayability without restarting the game? There was none whatsoever. There's no reason for me to want to play the game ever again, TBH. (which is why this was the first generation I stopped getting all three of the games. I stopped with Ruby.)