While I agree that TDK is a better film, I also agree with BB being the best Batman film.
While watching TDK, it didn't just feel like a Batman film. It's Nolan's Batman after all, and the changes made to the Joker and the rest of the city made it seem that much different.
While I'm not taking anything away from TDK, when I watch BB, I feel as if I'm watching a true comic book come to life, with scenes taken straight from the written pages (the bat call, for example).
I agree, it does have its flaws, but to me, it's still the best Batman film we have. TDKR comes close too, even more so than TDK, with the whole No Man's Land idea. Though TDK has The Long Halloween, I just feel as if the story itself is so unlike any comic. To me, I feel like I'm watching Criminal Minds: Batman edition.
There's nothing wrong with that, but to meet, BB will remain the best comic book movie.