I just finished the game, and despite listening to most of what the narrator said, I have no idea what was going on. I'm ashamed, but only a little. The narrator's comments were too disjointed or often played when I had to concentrate on dodging something on the screen.
From reading Alec's article and the comments, most people appear to have understood the characters' motivations. So:
1. What is the Kid's story? Is going through that horde/survival mode in the Bastion the only way to find out? (I gave up after a few rounds.) What was that (drug-induced) flashback in the middle of the game about? (The one where the kid does some mining.)
2. Who was Zia? I only got that she was an Ura raised in Caelondia. Was Rucks narrating the entire story to her?
3. Why was Zulf in Caelondia in the first place? Why were the Ura attacking him in the end?
4. Who is Rucks? What caused the calamity and was he involved? Where did he get that cannon?
5. Where did the cores/shards come from?
6. Why did the Ura stop shooting the kid as he carried Rucks? They knew all along he was trying to fix the Bastion and then the world; what changed in those last moments?
I also didn't feel any gravitas to the ending choice. Didn't see how it mattered, the game was going to end at that point anyway. (Also, no sadness. Which is sad in itself, because I really wanted to get into it.)
Again, I want to consider this a lack of attentiveness on my part, but honestly the narration just didn't work for me.