I loved the ending. And as you said the scenes with Alfred. It just felt like much of the movie was distant and uninvolving.
I actually went to the 'marathon' presentation, so I had just been reminded of how tightly-wound some of the moments in the previous films were (particularly when Batman is smashing Joker's face into the window and Joker just keeps laughing through his bleeding mouth "You have nothing... there is nothing you can do to me"). I missed that intensity this time. I missed not being safe.
To be fair, The Dark Night is clunky in places as well, and I don't buy that it was necessarily a better film than Batman Begins. With such obviously-cued lines as "No More Dead Cops!" and "They're having the same discussion on that boat that we are having!" (You would expect such mob-mentality dialogue to sound, I don't know... more improvised?)