By story yes, any attempt BW made to explore the ethics within the pokemon universe and question who is good and who is bad is thrown out window in the sequels to make room for join avenue, pokestar studios, the world tournament, the nature preserve and all of the other spiffy new post-game content. BW2 has by far the more innovative features, but BW has by far the more innovative story. The first BW will always be my favorite because of the way it portrayed character, even if the rest of the gameplay is barebones compared the sequels.
Team Plasma had a charismatic and sympathetic figurehead previously with N, and the organization appealled to our compassion. Team Plasma used the very love for pokemon that draws us into the series against us by posing the argument that pokemon may be better off not living under the control of humans. There was a logical argument to be made that pokemon were living in an exploitative system. Team Plasma in BW2 instead is maniacally loud and clear that they just want to plunge Unova into a frozen wasteland now.
In the first games you live out an ancient legend in the middle of what looks like modern day New York, becoming the hero of truth/ideals from the region's mythology. In the climax of the story you succeed where the champion has failed and stop the antagonist after tapping into a magic that had been long lost to the world, reviving the legendary dragon from stone in your hour of need through the power of your sense of ideals/truth, and defeat a character who is friend, rival and villain all in one, and your polar opposite.
The first game is literally about the balance amount of yin and yang. That's about as thoughtful as a main series pokemon game is going to get. I think it's not just the better written of the Unova installments, but has the best writing of any generation as far as I have played.