Something I've always thought about, in regards to the nitpicking, is it seems to all stem from the fact that Nolan attempted to make his Batman universe as realistic as possible. But when you strip everything away, and boil it all down, it is still a superhero movie based on a superhero comic.
I.e., Bruce Wayne escapes the prison and then in a short amount of time he's back in Gotham and stalking/confronting Selena. Oh, how does he get back so quickly? Honestly, yes Nolan wants his Batverse to seem "realer," but who cares how he did it? HE'S BATMAN! OF COURSE HE'S GOING TO BE ABLE TO DO IT!
The nitpicking comes from people pulling the superhero aspect of a Batman mythos and movie out of the equation and referencing the movie as a Memento equivalent or other "real" crime movie.
With The Avengers, no one nitpicks about a character being able to transform into an indestructible, green crushing machine or a Norse-god coming to Earth or a portal ripping into the sky and an invasion on Earth comes. But why not? I don't buy that "oh, it's a superhero movie more than Batman" or "Whedon didn't attempt to make it realistic" or any of that crap. The moment Whedon filmed scenes in which he tried to make his protagonists relatable, and give them layers and make them humanstic, he attempted to make his movie realistic. But no one nitpicks the fantastical aspects of the Marvel blockbusters? People simply enjoy them for what they are: entertaining, comic book fare that by default, isn't going to be pitch-for-pitch realistic.
I love Nolan, and I love his Batverse, and I love that he attempted to make superhero movies for adults. But why the hell do his movies deserve more criticisms than others in the comic book realm? Enjoy them for what they are and if you get more a emotional resonance out of Batman than other superheros (like I do), great! If not, that's okay, too. But all blockbusters are riddled with plot holes and Batman can do the things he does...because he's freaking Batman.
Just as Wolverine can do the things he does because he's freaking Wolverine, and so on.