Jim Emerson has started a very interesting series of posts on The Dark Knight. I thought it was a very good, but flawed film, and, though Jim thinks it's a bad movie, the issues he raises tie into why I don't think it's a very good film, full stop, let alone a great film.
My take is that it's a sloppier piece of filmmaking than Batman Begins (and a much sloppier piece of filmmaking than The Prestige), but that the many moment-to-moment examples of spatial/plot incoherence are overwhelmed and - to a certain extend - made irrelevant by the movie's thematic and emotional intensity and specificity. Or, rather: the incoherent moments are overwhelmed by the intensity and it is the specificity of how that intensity is achieved that makes it easy for those of us who like the film to ignore them even when, after the fact, someone like Jim points them out to us.
I think that you can do these or similar kinds of exercises with other movies on this tier - "very good, but flawed" like No Country for Old Men or There Will Be Blood - but I doubt they have much effect in terms of changing a sympathetic viewer's mind. This can still be a useful and/or interesting conversation to have, but, at one point in the comments Jim says that "the movie" comes before "don't like", which I think is true only to a certain extent. Most people - critics included - do not watch a movie with a mental checklist of how all the little pieces are falling into place or how they're not falling into place. Rather, I think we're always moving between the little details and the Big Picture that's coming together in our heads. In fact, without some sense of the Big Picture, we can't even begin to make sense of the little details.
And there are some movies that require you to buy into the Big Picture upfront, because, otherwise, none of the little details are going to make sense. Take A History of Violence or Eastern Promises: if you approach these as if they're meant to be "realistic" crime dramas, they'll probably come off as sloppy, incoherent, and ludicrous. I don't think either of these movies has any major flaws of the kind Jim is talking about (or I was talking about here or Dan Sallitt was talking about here), but if you're not a sympathetic viewer, every moment probably looks like a flaw.