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I think that BW2 was the best in terms of features (you'd hope so since it's the latest game) and Platinum/BW had the best story.
However, my favourite games would have to be HGSS. I played Heart Gold and I absolutely loved it. The menu and user interface was beautiful, the graphics were great (for a pokemon game), pokemon following you made them feel that bit more special, you get a bit of nostalgia playing it, the managed to keep the essence of the originals while adding all the recent features and improving upon the original. It gave me one of the best feelings whilst playing it. It wasn't perfect, but it's still my favourite game. Emerald was probably come second since the region was diverse and fun to explore. If they remade RS in 3D while fixing it's errors and updating the game, I reckon it would take the top spot on this list.
