I'd have to say Black and White had the best story because of the twist in the evil character. I liked HG/SS as well but B/W is currently on the top of my list
I loved the story for Pokemon Black/White because there were moments where I felt excited, sad, adrenaline rush, upset, etc. I really loved Black/White's story on how the perspective of N and Team Plasma go against the player's thought on Pokemon. I found that to an exciting contribution to Tue general story. Hopefully, Nintendo and GameFreak will continue to make such fascinating stories to the new games in the Pokemon franchise.
I've been playing through Gen II and I've been loving it so far. I just think its really awesome how it links to Gen I. However what would it be like if there was a pokemon game with bad guys or enimies and it was you trying to be the best, like no one ever was?