I agree with you, to a point. It gets on my nerves whenever people talk about how Nolan is "afraid" to use villains like Mr. Freeze, Clayface, etc. What the hell is he afraid of? He knew going in that he was going to have a limited number of films, that he had a certain vision for those films, and in all likelihood, he probably knew the villains that would best fit that vision beforehand. So because he makes movies with a more grounded tone and isn't going to toss every villain in the rogue's gallery in there, he's some sort of coward? Was Burton afraid of using Egghead or King Tut?

The absurdity of it is almost like thinking Adam West's Batman should have had a Joker with a cut smile.
However, I don't think Nolan's movies are infallible or above criticism. While I don't think Nolan should be attacked merely for giving us a different take on the character, I think that fidelity to the source material should at least be given some consideration. I mean, that would definitely be the case if this were a movie based on a novel. Being based on a 70 year old comic book character does complicate things a bit, though, because there's
so much stuff to draw from.
But you can narrow that down to the past few decades since they're primarily what this version is based off of, and in those past few decades, Gotham itself has become as much of a character as Batman and his villains have been. Just mentioning the words Gotham City to a fan of the comic conjures up all sorts of art deco imagery, gargoyles, buildings cluttered together, urban decay, blimps, etc. I wasn't expecting much of that in TDK, but to go from the grungy, rainy city in Begins to the clean city in TDK was a bit of a shock, and arguably, a step in the wrong direction. Yes, I know there were reasons for it, but they made Gotham less interesting and threw away what little sense of individualism the place had. This made it more of a frightening place on the one hand, since it could be any city in America this is happening in, but on the other hand, it was a total snooze to look at, even if it was impressively filmed in some parts. None of this takes away from the fact that TDK is the best comic book film that I've ever seen, but if anything, I think it gets so much criticism and nitpicking because people watch it and think, "Wow.. that was amazing. But if they'd just changed a few small details, it would have been PERFECT."
And this really doesn't have much to do with my point, but I gotta say that comparing all the sterile, open stuff in the film to Kubrick does nothing for me. To me (and I know this will be an unpopular opinion), Kubrick's probably the most overrated director in recent history. I've never seen a film of his that I can honestly call "bad," but chances are, if I see one of his films that I've already seen coming on TV, I'm going to skip over it in favor of something with more heart. The whole "cold, isolated" thing just bores me to tears, and I've come close to falling asleep while watching some of his movies (his version of The Shining in particular. And I loved the book,) and I'm not someone with a short attention span. I just consider myself an average Joe when it comes to watching movies. I've had a couple of teachers who taught me how to analyze film and things like that, and sometimes I pick up on symbolism (and when I do, it's pretty awesome), but I don't go out of my way to. That's not what I watch movies for. To quote Joker in Mad Love, "If you have to explain a joke, there is no joke!" If you gotta explain to me why a movie's good, it's probably not
really that good. Kinda rambling, but there's my two cents on that particular issue.