Oh, I agree on The Dark Knight being clunky as well, my feeling is that I enjoy Batman Begins more because it's main story feels more coherent. The Dark Knight is very rambling and silly in places in ways that undermine it on repeat viewings.
And to be honest I always found the ferry boat sequence quite simplistic. That just did not at all work out any way that didn't seem obvious from the start.
I have thoughts about the ending but I don't want to ruin anything and I feel some might be tempted to look inside a 'spoiler' alert but I have a couple of major issues with it in as much certain characters seemed to me to get very 'easy' endings, as if Nolan knew he was capable of better but just went easy to get things wrapped up.
Without giving detail I don't know if that would just be me.
I also thought that the script was spectacularly unsubtle and never quite comitted to any of the dozens of themes it tried to squeeze in. It was like, 'Let's throw in a whole bunch of stuff but not really get into any of it'. I mean, on a certain level I enjoyed the film. I just can't say a lot without spoilers being made about where it didn't work for me.
I would currently rate it last out of the three anyway.
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courtesy of Saquist