"A guy who has a cellphone, inside his body, which is a bomb. A tiny bomb capable of blowing up an entire building, but conveniently doesn't kill the Joker."
It didn't really blow up the building, and the bomb was in a separate room from the joker. The Joker was further from the explosion than everyone else. Also, I'm not positive, but I believe the cell phone was just the trigger to the actual bomb. He had a lot of lumps in his stomach.
"When arrested, the Joker has about a dozen knives on him. You think they would do a more thorough search, but yet the Joker keeps a cop hostage with, you got it, another knife."
He is actually holding a broken piece of glass to the cop's neck, not a knife.
"After a huge "upgrade" in armor, Batman still gets stabbed in the stomach by the Joker."
Well his goal was to move quicker, and Lucius tells him with the new suit he'll be more vulnerable to knives and gunfire.
"How could a criminal on trial bring a gun into a courtroom? And when disarmed, why would Dent give the gun to the defendant? "
I believe he unloaded it and was shoving it in Maroni's face because it was made in china. Still not the best move though.
"How in the hell does the batpod get out of the nearly indestructible batmobile?"
It like. . . morphs. . . and . . . was it in there in batman begins? I don't know, it was badass though. I really like how it was very machine like and clunky to eject it, as opposed to fast, elegant, way too close up and illogical like transformers.