I'm going to be very boring and say Gold/Silver/Crystal. In my case, specifically Silver.

I think one of the main problems I have with the later games, which I've played and continue to enjoy (I finally got around to playing Pokemon Black last month), is there are too many Pokemon. The designs are still reasonably imaginative and interesting, but I don't think they have the same quality, by and large, as the first 251. In addition, I'd also say that 251 was a much more manageable number. With 251, I was more excited because I believed that I could actually complete my Pokedex, because realistically there were only four games I'd need (or ideally, one friend with Blue/Gold while I had Red/Silver).

I also liked the variety of locations. I really quite like Kanto as a region - its towns, gym leaders and locales are all reasonably close to my heart. I especially liked the ability to visit both Kanto and Johto - something I've wished subsequent games would let you do. While it wasn't quite like getting two games in one, it provided much more to do after beating the Elite Four. Generally I find that in the Pokemon games I lose interest after beating the Elite Four - G/S/C kept me interested. 16 gyms also gave you the need to have a well-rounded Pokemon team. I tend to use the same Pokemon the whole way through the game, rather than switching based on my needs, and so it gives me an extra incentive to need to have a team that can cope with any situation.

The games also introduced a number of innovations which I liked - things like the PokeGear, shiny Pokemon, legendary Pokemon you have to chase around, day and night, events throughout the week, etc.