Caution, spoilers below:

What bothered me initially about the film was that the dreams just didn't seem very dream-like. Most of the dreams were too detailed and clear, and seemed too strict in following the logical patterns the film set for them. Most of the dreams lacked the surreal touches, the dreamy fuzziness as portrayed in other much simpler films like "Dreamscape".

Also some important rules followed by the 'induced' dreams of the film appear to only apply to those types of dreams and not to natural dreams... I know this may seem obvious but I think the film unnecessarily blurred the line between the 'nature' of the induced and natural dreams leading to some confusion.

Another thing I had a lot of trouble buying into was that the characters involved in multi-layered dreams left behind some sort of 'ethereal' bodies asleep at the lower dream levels.

In other words, when their minds move on to another dream level I see no logical reason why they would be leaving behind some bizarre dream-sleep bodies at the lower levels.

They might DREAM that they are waking up from one level to the next but to say that they actually leave behind some sort of sleeping dream-body seems silly to me.

e.g. I can go along with the idea that the 'Chemist' might experience the others as being in a drug induced sleep while he's driving the van during that wild chase scene. But why would the others have any dependency-on the Chemist's perception of their sleeping bodies at the lower dream level?

One aspect of the film I liked a lot is that there are hints now and then that we are still actually watching a dream when the characters are supposedly awake...

Didn't the Cobb character say there was a danger in composing a dream too close to your real-life because you could no longer distinguish between the two?