I think the movie was designed to leave an audience arguing for years.
That said, I fall in the "the whole movie was a dream" camp. While in "reality, numerous characters tell Cobb to "come back to reality," "wake up," and "who are you to judge what is real?" We are also told from the outset that a totem is used to judge reality from dream. In the third act, we learn that not only is Cobb's totem not his, but he admits to tampering with it. One character points out to another that Cobb, our point of view in this story, breaks every rule he sets. Cobb doesn't know up from down, or reality from dream. And every character and situation in the film is some variation of him talking to himself.
Thing is all Mal has to do is perform a kick back in reality to get Cobb out.
The one place that Inceptions seems to fall apart is the jeopardy of limbo. Despite all the hand ringing, according to the rules of the movie there really shouldn't be much danger to it at all.
This is the biggest questionmark unless the whole movie takes place in Cobb's limbo, in which case he could already be in a coma and beyond help in reality and Mal is trying to snap him out of it. This could explain why she doesn't appear straght away if she has to track him down in Limbo. It doesn't explain why she acts a bit crazy though so I'm more inclined to think she is a representative of his own subconscious trying to wake him up because the real Mal can't get deep enough.