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Black and White did some really interesting things, and that's an honest opinion considering I might be called a nostalgiafag for R/B G/S.
Though Team Plasma felt underdeveloped, N's character was marvelous. He was prince raised in a eerie, captive environment lead to believe his vision was his own and what he was doing was right under the control of a manipulative Religious leader.
Plus, the final battle taking place AFTER the Pokemon league was pretty damn intense.
Honestly, it might have had the best story out of the entire series.
That being said, the story in X/Y felt tacked on. The focus this time was on taking an adventure with your friends. They were going for the traditional JRPG feeling, where you have a cast of characters who interact throughout the journey and gain an attachment to (and they had a love interest to boot, unfortunately it wasn't the one most people wanted). However, the confrontation with Team Flare was INCREDIBLY underdeveloped. Lysander's motives could've been corrected had the Prof given him like five more sentences, the Prof says it himself.
It felt... too clean and simple as opposed to the complexity Black and White had, and that was it's downfall.
Sidenote: I am pretty disappointed with the post-game content. Especially since it has the least since R/B. I still think it's excellent and the fact that it is a complete 3D world and the battles are stadium style still give me a massive boner.