Here's the way I look at it.
A fictional story should follow its own rules. Let's take "The Good, The Bad, and The Ugly." The idea that someone would let himself be hung, trusting the other guy to be able to make that incredible shot over and over and never miss, is nonsensical. But we in the audience accept that premise for the sake of the story. We'd be disappointed if, halfway through the movie, an orchestra appears in the middle of the desert and they do a big musical number.
"Sky Captain" was ridiculous because of the way the story kept shifting and the rules kept changing.