I guess I disagree with you about Flight. Let's see...
We do get to know Whip, who just happens to be an alcoholic and drug addict; which in turn means he's a master manipulator, a chronic liar, in stubborn denial, and is running away from the truth about himself. (This behavior is contrasted with the fact that his piloting not only didn't cause anyone harm, but that no one else could've prevented the deaths of all, with his obviously expressed, personal guilt.) The question his son raises in reference to this point is the question all of us must answer at some point, alcoholic or not, and hopefully aren't too afraid to face. Alcoholics are too afraid, which is the point of the movie.
Can you provide examples of the script being "a bit of a shambles"? Personally, I liked it a lot. As for characters being included to serve particular purposes, what characters aren't? I guess it's a matter of taste when symbolism is used whether or not it's too obvious. Again, I didn't have a problem with how Goodman's character, or any of the others, was shown. I feel the religious motif was there to reinforce Whip's progression in perceiving reality from arrogant and overconfident toward total humility.
I find it very appealing that his final decision is based on an inability to allow the memory of a friend, the flight attendant, to suffer. He recognizes he has a moral obligation to the truth. Here, who he really is, which is alluded to throughout the story, via his initial post-accident repellence from alcohol and drugs, through his self-flagellation, and his growing struggle with the idea of changing, finally emerges.
In the end we are encouraged to understand that if we face ourselves, the answer to the question his son asks is only a matter of review.