The top as totem doesn’t make sense according to the logic of totems as exposited by the characters in the movie. A totem is supposed to have a unique, unpredictable property in the real world that no architect would know to replicate in a dream world. Hence, the loaded die, etc. But the top has a unique property in dreams that can’t be replicated in the real world.
It appears that the spinning of the top can’t be taken as a reliable indicator of anything. Cobb tells himself that it indicates something–but Cobb is decieving himself.
Put this together with the identical appearance of the children at the end of the movie–their clothing, posing, etc–as compared to their appearances in the rest of the movie, and it seems clear that the whole film depicts Cobb’s dream.
The concept of Limbo also doesn’t seem to bear out in the film’s events in a way accurate to its description in exposition. Supposedly, if you die while sedated, you end up in a chaos, trapped until you finally wake up. But we never see that chaos–it’s thoroughly sensible dream-world architecture all the way down. Yet, I do think the movie depicts Limbo. The entire thing is set in Limbo. The chaos is the chaos of not knowing the difference between dream and reality, even when you know there is such a distinction to make. (Normal dreams aren’t in limbo, because in normal dreams you don’t even realize there is a distinction to make. You just have your dream, then you wake up. In limbo, you know you might be dreaming, and are constantly trying to wake up, and are never sure if you’ve succeeded.) If killing yourself while unable to wake up puts you in limbo, and if, once in that state (as we see depicted in the film) you still find yourself in a fairly sensible dream-world architecture, then what happens when you kill yourself while in that state? Instead of waking up (since you can’t) it seems you must instead go to levels even deeper. Getting out of a dream while unable to wake up just puts you into a deeper dream.
I think this is what happened to Cobb. He’s in limbo, working through psychological issues, trying to be awake but unable. And maybe some of the other characters are from the real world, trying to help him out of the dream (but I wouldn’t stake any money on that–they may all just be projections of his, part of his dealing with the whole dream/reality issue). After all, plenty of characters exhort him to do things like “come back to reality,” most esp his dad and Mal. (And the scene with him talking to his kids on the phone–probably just projections but maybe he’s hearing his kids sitting by the hospital bed he’s laying on while in a coma. “You’re never coming back, are you dad?”)
Ultimately, though as you can see I’ve got a theory about “what’s really happening” in the film, I think the best thing with this kind of movie isn’t to ask “what’s really happening” but just to ask what the events depicted mean for the people depicted. Did the top keep spinning in the end or not? As I argued above, even in the film’s logic, it can’t really matter. And ignoring the film’s logic, I would still think it can’t really matter. Cobb has come to a place where he can be happy independently of the question whether he’s dreaming or not. (Note he ends up ignoring the top). That’s his big transformation. The question isn’t whether he’s dreaming or not, the question is how should we feel about him no longer really caring?