While I don't think it was bad, I do think it was the weakest of the three.
I place it in second, because I could never get over the "Batman is a ninja! That's so cool!" idea that they used in the first one. I never followed the comics, so I don't know if this also happens in them, but I don't think Batman needs ninja hype to be as cool as he is.
2. There are lots of little plotholes. For example: in the beginning, Bruce has to resort to a sort of mini-robotic brace for his leg to compensate for his damaged knees. But later on when he's recovering from a broken back (and I'm not even going to get into the details of that), once he's "recovered" he can somehow do crazy acrobatics all on his own again. Apparently the cartilage in his knee magically regrew?
The only explanation, for me, is that Bane only broke some of Batman's vertebrae, not his spine. I remember the prison doctor mentioning that one of Bruce's vertebrae was sticking out, but I don't remember him saying that his spine was broken.
But this would only explain it partially, and the thing about his cartilage was a really awful plot hole.
3. Bane was kind of wasted. Bane had the potential to be a really interesting villain, but they completely undermined his history as a strategically-minded, charismatic revolutionary by just having him be a second-in-command who serves as a public figurehead.
I don't think he was second in command. It seemed to me that Bane and Talia shared the top of their hierarchy, and that both had the same ideals. The only thing I'm not entirely sure about is whether they were lovers or just friends, because in the end she calls him a "friend".
crying Alfred was obnoxious.
Yes. And in the end, that was just an excuse in the plot to have Alfred out of Gothan when Bane's takeover took place.
the class conflict.
It seems like Nolan injected cursory mentions and vague lip service to the idea that there is a class struggle, without ever developing that idea. It's like he wanted to say "See how topical and astute I am? I'm bringing up the issue of class warfare!" But then he doesn't ever get deeper into the idea, or make any kind of point with it. Like an "awareness campaign," he seems to want points just for acknowledging its existence without having to do any actual work or committing to a specific stance.
I strongly agree. This was a huge plot hole, and even though filling it wouldn't have made much (if any) difference to the rest of the plot, filling it would have substantially improved the quality of the movie.