RSE would have been my favourite the sprites weren't so damn ugly. GSC's sprites are classical, and had such great poses, even with new Pokemon *I always find when a new region is brought out, the new Pokemon have such boring poses*. I enjoyed the addition of the shiny Pokemon, because it just gave awesome variation to your teams, if you had the patience to breed for more.
I loved the music, and I'm so disappointed that the beta GSC remade music for RSE weren't ever used, not even on Leaf Green *they actually HAD a legendary beast battle theme, and they never used it!!* I enjoyed the simple yet cute graphics, and even now I love to create maps with the GSC tiles.
I loved the storyline, and the game isn't as difficult as newer games, because EVs and all that crap weren't a big deal, because they didn't have them. You could choose your team without having to worry so much about what natures they had to have, and how to train them right, etc. It was FUN.
Put simply; Crystal especially, was, and still is to this day, my favourite Pokemon game to play.