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I think BW2 had the best story. I liked the fact that there was this whole "good Team Plasma" and "bad Team Plasma" dynamic, it really makes you question how redeemable the evil teams are in the games. On top of that, I really liked the rival's backstory. It actually provided a reason for his attitude. The only problem with, I think, is that you need to have played BW to understand just how great the story is.
I feel like the whole 5th Gen games combined, there was just so much that intrigued me about Team Plasma and the Memory Link in B2/W2 helps tie both stories together. It was always the one generation the story had always impressed me with.
I know plenty of people are going to disagree here but I loved XY's story, especially Kalos' history. It felt really tied in to the region - the grandeur of the past in Parfum Palace, the high costs of Lumiose City, the constant spending of money on customization makes it almost seem like Lysandre has a point. But by charging for the chance to stay alive, he only ensured that only the worst of mankind will live on...
Also I liked how it essentially reflects on so many traits of France, referencing WWI and WWII in different ways. Makes the history geek in me happy.
I feel like the whole 5th Gen games combined, there was just so much that intrigued me about Team Plasma and the Memory Link in B2/W2 helps tie both stories together. It was always the one generation the story had always impressed me with.
B2/W2 felt like the best plot to me. I wasn't crazy about B/W's story, but I did like how B2/W2 led off from it. I also really liked the storyline for D/P/Pt for how relatively simple it was. Buuut... I never really put THAT much attention into the story of Pokemon games. They usually feel very samey and not that engaging, sort of like a device to keep the gameplay progressing.
I'd say gen 5 as a whole featured the best story of all the main series games. Not only did they actually put a lot more thought into how the story unfolds, but also switching things up with certain plot twists made the games definitely stand out.