I couldn't agree with
@Ignition more. BW didn't handle the morality and ethics side of the plot very well; it kept skirting around the question of whether or not battling is detrimental to Pokemon overall, and preaching friendship at every moment possible. It didn't help that Team Plasma and Ghetsis were very obviously evil - remember the scene were some grunts kicked a Munna early in the game? It would have been nice to see Team Plasma shown in a more ambiguous light, like N was. That would have made the "plot twist" that Ghetsis was the evil one much more interesting.
The high points of BW's plot are definitely its characters - and the ending, despite what I said before. The sequence where Plasma takes over the league and the final showdown with N are still amazing to play through today, even if - now that I've grown up - the rest of the story isn't that great. Seeing how N's life changes for the better, and his reflections on his journey, was surprisingly moving. Cheren, Bianca, the gym leaders, the elite four, and the professors were also fleshed out much better than those of past generations, with several of them getting backstories and development. While the execution of their character arcs was nowhere near perfect, it was a first for the series and better than nothing.
(The exceptions to "BW has well-written characters" are Anthea, Concordia, and the Seven Sages... but I think the rest of the cast makes up for that.)