I am currently doing a Begins edit and feel basically obligated to remove "nice coat" and "that's right you better run," but I'm not so sure about removing ALL the humor, and I've felt the same way as you before about the tendency to basically purge movies of any jokes. I think the nice coat part kinda breaks the intensity of the big reveal of Batman and the better run is just poorly delivered by Holmes and feels very cliche. Maybe the big problem with the Dark Knight trilogy specifically is that the movies are trying to go for an uber serious, almost grimdark tone, and the humor feels almost Marvel-y, especially when they try to lampshade stuff the audience might find ridiculous, like making a joke everytime Batman (or Catwoman) disappears. A lot of the jokes are also just really cheesy like when the Harvey Bullock-stand in (forgot his name) literally says "have a nice trip, see you next fall."