To Huh?'s questions:
I agree with the other poster who said that Mal was across the way from Cobb in the window of the hotel to show their separation and to show that Cobb couldn't get to her. It could be a U-shaped building where she just walked around the ledge to sit and wait for him and to have a face to face conversation.
The part of the audience I was with all seemed to indicate that they beleived the top was starting to fall at the end. But I do think it was a little ambiguous.
Cobb and Saito get out of limbo the same way Cobb and Mal did. They shoot themselves with the gun like how Mal and Cobb killed themselves with the train.
As for Mal being in many of the dream levels...I don't quite remember how each of the people work in in terms of whose brain hosts the world, how the architect's plans get in there, who can control stuff while they are in, but it seems that throughout most of the movie no matter who is hosting the dream, Cobb's wife or kids can show up and affect the "stability" of the dream.
As for the air vents, and the arctic troops changing focus, I think this is just like any of the dreams where the "projections" in the dream come to evict the intruders. At some point the intruders cause enough "strangeness" that the projections can identify them. Arthur and Ariadne weren't doing anything but sitting in the hotel lobby, yet the projections kept looking at them.
As for the heroes not getting shot, I think it was more a question of skill and preparation (and a little bit of just being the heroes) that keep them from getting shot. Much like in the Matrix, knowing you are in a dream is powerful, you can bend the rules. From the very start (in Saito's first dream) Cobb is totally kicking ass...I think it just a thing about being in the dream being able to choose victory like being able to bend the world on itself.
As for Mal keeping the totem/top in the safe, I think the point was that she didn't want to believe that the limbo world wasn't real, she didn't want to go back to reality, so she had locked it away. Cobb realized this when he found the safe.
Just my thoughts on those questions.
I would like to see it all again to get second impressions.
Edit: I think Cobb took up his wife's totem because of his guilt. Also, the Mal that tells Cobb that his world of "shadowy figures" pursuing him is the Mal of his subconscious, so she would have access to his memories. If an "objectively" real Mal said it, it would be evidence that she is right, but that was just Cobb's impression of his wife's opinions/beliefs talking.