(There are times, though not often, when I do notice those things because they are especially well done. This was true in Inglourious Basterds, for example, where there are sequences where the pacing, or the camera movement, is so wonderful that I just enjoyed it for itself, paying less attention to where the characters were going or why. But I plan to talk about that next time.)
But in any case, there is the experience of seeing the movie, and then there's the experience of thinking back on it.
With Prometheus, the shift from experiencing it to thinking back on it happens almost immediately. When I was leaving the theater, the general buzz around me was "Hey, now, wait a minute. Why..."
There are certainly moments in the movie when any person of pretty much any life experience would wonder at how stupidly the characters (supposedly trained scientists and professional space pilots) are acting. There are whole blog posts devoted to the various bad decisions they make, but the short story is that at pretty much every point the characters do idiotic things and needlessly expose themselves and others to danger.
In general (for me and for a lot of other people, as far as I can tell), there are also many sequences where you're just sitting there, gripped by the immediate action. But then there's that moment when the credits start, when you inevitably begin to realize that many of the incredible things you've just seen make absolutely no sense, many major actions and decisions were apparently completely random, and many big questions were raised and then forgotten about.
So, much as I enjoy the experience of watching Prometheus, I'm not panting for a sequel. I have no interest in finding out what happens next, because nothing in the first movie meant very much. There are unanswered questions, but they're not that interesting (and I would bet that really satisfying answers won't be delivered, no matter how many sequels there are).
(Well, I might go see it, but that's mostly because I would see Noomi Rapace in pretty much anything. 🙂 )
So, I think the lesson here is to write stories which grab the reader at the time of reading (which is the most important thing), but also reward reflection afterwards. After all, you want your readers to come back for more, right?
I talked about this here (scroll down past the part about the Chicago Manual of Style).