Err...well, Crystal gives me a warm sense of nostalgia (despite the fact I've only ever played the game on ROMS).
On the other hand, Emerald managed to combine both nostalgia and a little more modern features and was really "magical" to me, as cheesy as it sounds. I felt as a little kid that I was the boy in the game, walking around the mystical Heonn region.
Black was the most modern of all so it also deserves credit, but it loses brownie points because all the nostalgia is now lost. This would've been forgivable if Black was incredible and amazing, and it is to an extent, but I think if I was designing the game I could've expanded the updated graphics and features to their fullest. Maybe it's just me.
I'm really not sure...if there was a game based on the anime (any season, up to Advanced Generation--Diamond & Pearl got sort of icky) that that would be my choice.