Honestly, Batman taking the fall at the end never bothered me. You can't have Joker taking it, because too many people know That it was only Gordan, his family, Dent, and Batman were there.
As far as the trilogy goes, TDK was the strongest while I had both Batman Begins and TDKR at 8.5/10
TDKR I initially rated higher but it dropped down a bit during repeated viewings. The dialogue is just super bad at some parts and I thought they could have built up JGL's character a bit more. Still, the scope of the movie was amazing, the cinematography was beautiful, the score was awesome, ect. The production values were some of the best I've seen in a movie. The ending was excellent too. Perfect way to end the trilogy.