It not the plot holes themselves, it's wether or not they break suspension of disbelief. In Star Wars and the dark knight, you don't really notice them at all because you are too invested in the story. But in a film like Prometheus and TDKR, they pull you out of the movie because they add up too fast and become the focus instead of the story.

Plus, Nolan's films have a reputation for being too talky and more based on ideas instaead of visuals. In a visual medium like film, that's not really encouraged.