Here's my take on a couple things:
Cobb (first time), his wife, and Saito age in limbo because they believe it's real, so their minds take over and do things as if it were real. If they didn't age, they would be able to figure it out. Cobb/wife were younger again on the tracks because they realized it was a dream (he realized and made her realize), and thus took control of their aging again. I would be more satisfied with this explanation if in the final scene with Saito he looked younger again after seeing the top. Cobb didn't age the second time because he had experienced it before and could realize it was limbo.
It bothered me how they jumped off the building in level 4 to go up to level 3. I thought the explosives in the fortress were to bring them back up, since everywhere else in the movie you had to be kicked from above. Though, the kick was supposed to cause a feeling of falling in the level before, so causing yourself to fall makes sense. But then, what were the explosives in level 3 for, and why couldn't they just jump off a building instead of making elaborate kicks from above?
I think the whole movie was done on level 1 (so the whole movie was a dream), as Cobb tried to convince himself it was real. He talked about how deep him and his wife went (dream within dreams) but then when replaying it they killed themselves and went right to the hotel room. Shouldn't they have gone up level by level? And the whole spinning top thing was a little bothersome. Why would the top always spin perfectly in the dream? Just because they said so? Just because HE said so (when they tried to make clear he may not even be able to distinguish reality)? And even if that makes sense, it seemed that every time he spun the top in the 'real world' someone barged in and he knocked it himself (unless I missed a time that he let it drop).
Finally, the whole totem thing bothered me too. So Ellen Paige had the chess piece and carved something in the bottom that no one else saw. So in a dream, she can check to see if it is there (or even the weight of the die). So who put the chess piece there, the architect, or the dreamer? If the architect, they would have to know everyone's totem but only partially (which I guess makes sense), and if the dreamer, then it would be exactly as they remembered it. If it is the architect, the totem thing doesn't work to protect you if you are put into a dream by someone else, since you won't know if you lost it or if it just wanted created in the dream (maybe that's why they NEVER let it go though).
All in all though, loved the movie!