I would guess that's due to Nolan focussing on great visuals rather than the underlying ideas. I did enjoy The Prestige, but often his stories become somewhat nonsensical e.g. Inception's plot doesn't really make any sense when you look into the characters' motivations etc.
Yeah half of his films are super flashy and quite watchable but you really have to turn your brain off to avoid thinking "what? that makes no sense" constantly. Inception, Tenet & Interstellar at least.