Not gonna lie, I really adored B2W2's story... However, the only main series Pokémon game that ever had me on the edge of my seat was BW.
BW had a large, fleshed out cast, and the characters were very well planned out (and of course, they had good character development as well). In addition, the plot of BW had a greater sense of progression, and it was very climatic when things were rough, while being deeply emotional when the times were low.
As for B2W2, the plot was DEFINITELY better than your average Pokémon game, but it reverted back to having a relatively simple plot. Despite the fact that I adored B2W2's story, there actually WAS one problem I had with it -- Purrloin. To be honest, I think it was too ridiculously convenient (not to mention wayyy too unrealistic for an already unrealistic game) that the Shadow Triad happened to be in possession of the exact same Purrloin/Liepard that they stole from Hugh's sister, despite the fact that Liepard is an incredibly generic Pokémon that plenty of Team Plasma members use.