Crystal is my overall FAVORITE version.
Though the Ruin Puzzles to unlock secret messages with the unknown resulting with holes in the walls.
I know the puzzles form Entei, Suicune, and Zapdos (for some stupid reason), but they are JUST SO HARD because of the 24 bit patterns. RRRGH.. a kid who lives across the street showed me on his game once, and did it in 2 minutes. It reminds you of Rubik's Cube.
No, I'm NOT a Pokemon freak/addict. I just remember it very well. It's all because on my Crystal version, I had 1002 HOURS OF GAME PLAY. YES, THAT FREAKING MUCH.
(until my brother freaking started a new game D