Just finished it and the ending was too abrupt for my liking, but I like that it wasn't exactly a happy ending either. There has been a lot of bickering in this thread whereas I feel you can take away from the ending what you want.
Joel made a selfish decision. Some people would have done the same thing. I wouldn't have, and I was angry at his selfishness, but I don't have to agree with the choices fictional characters make. He's not my surrogate.
@bisonhero: I think it's another case of exaggeration to make a point even if they do have strong powers. In investigations 2 von karma manipulates the crime scene with police supervision. It's supposed to be ridiculous and feel like injustice.
@oni: I don't think it's any more far fetched. The 3DS game is in some ways more frustrating because the entirety of Apollo Justice is about changing the legal system and it is completely forgotten about as soon as the game finishes. They figured out the problems, implemented a test for a new system and then never discussed again.