1. Story was dumb. They tried to do deconstruct the whole concept of capturing and battling the creatures that everyone has been making fun of for years anyway, but because it's still meant for children, they boil the morality down to "actually, there's no problem at all, the main villain doesn't even believe in Pokemon liberation, and the other villain of the group turns out to be good and falls in line with the status quo."
2. It was very linear and the game loved to handhold you a lot of the way through the game. It's got, in my opinion, the second worst opening in the series with how slow and tedious it is, and from there you've got to do things like the whole "find the Munna getting abused by Team Plasma" and "wow, look how creative the gimmick for our first gym is, oh and here's a type effective Pokemon for free to reduce the challenge" within the first hour alone. And from there, every gym leader seemed to be off doing some unrelated bullshit that you had to watch them do before you could tell them to get their asses back to the gym so they could do their fucking jobs.
3. No Battle Frontier and practically no end game content means once you beat Black and White, there's little reason to keep playing. There wasn't even any equivalent to Pokemon Colosseum or Pokemon Battle Revolution to tie in to the handheld experience.
Keep in mind, I actually liked these games. I liked them a lot more than Diamond and Pearl, which were slow as shit, had the most annoying rival in the series, with a way edgier plot that B&W had and even worse designed mons. The only saving grace it has was the underground and the fact that it's the gen that gave us the physical/special split. Still, you can find problems with every generation, which is why genwars are fucking dumb.