With The Dark Knight, in particular, I found myself frustrated at being transported between the gorgeous, native 70mm photography, and the (still gorgeous) 35mm photography that the majority of the film was shot in. What they did was, the film started out in native 70mm for the opening sequence, and then, when they switched back into 35mm, the film suddenly had a letterbox effect to it. It would be like, if you were watching a film on a standard 4:3 television set, and the image kept switching between full screen and letterboxed widescreen.
Why this is so annoying has to do with the fact that I've already seen this film twice in a regular theater with standard 35mm prints. The 70mm stuff looks fine, down rezzed to 35mm for exhibition, with a single aspect ratio for the whole film. But, for them to keep going back and forth between aspect ratios during the film became REALLY annoying. I know its expensive, but they should have just shot the whole thing on 70mm. It would have looked AMAZING. Or, shot the whole thing in 35mm. They did it for Batman Begins, and I can't think of a single moment in that film that I can complain about.
My other problems with IMAX just stem from the logistics of the theater itself. There's very few "good" seats in an IMAX theater, and if you don't get one, you spend your whole time with your head darting around, trying to take in everything that's on screen. And, usually, you can't. A lot of films on IMAX are action films, and by the time you're eye and brain are working in conjunction with each other to recognize what's on the screen, there's another split second cut, and your brain has to refocus. With cuts maxed out, sometimes, at just seconds, and a two story screen to take in, it just isn't enough time.
I like the big screen of IMAX, IF, and only IF, I can perpetually have a perfect viewing experience. But with IMAX, there's so much more to throw that off. I still love Dark Knight, but I can do without IMAX.