I won't pretend to contribute in great detail to the heated debate on whether this film is a masterpiece or overrated. I would merely like to make one specific point, not often addressed by other reviewers. When I finally went to see this film, the decision was mostly based on the many reviews which said that the cinematography in this film was similar to Stanley Kubrick's, and I have to say, I strongly disagree.
As you will have guessed from context, I'm a Kubrick fan. That is not to say that I was disappointed by this aspect of Malick's film or thought it was not beautiful in its own way. But Kubrick's method was purist to a point which earned him the reputation of being a control freak. With regard to his images, this means that they look sometimes calm, sometimes tough, that they can be poetic or ironic or frightening, but that they are always painstakingly composed in a manner that heavily relies on symmetry, clarity, and, to a certain extent, simplicity (think of the flattened, painting-like zoom-lens shots in "Barry Lyndon," the hallways and the labyrinth traveled and scanned by the steady-cam in "The Shining," or the court-room scene in "Paths of Glory"). Kubrick's shots look inevitable, as if this particular object or event could not have been looked at in any other way, but they seldom look spontaneous.
Malick's compositions are far more spontaneous and far less strategic. They derive a good part of their strength from their sheer visual spectacle, which is precisely why they depend so much on the viewer's readiness to absorb them rather than reflect them. Like Kubrick, Malick often makes use of defamiliarising techniques like wide-angle lenses and unusual camera positions, and he also likes to play with shadow and light, but Malick uses his heterogeneous range of techniques less in the name of a composition which comments on its contents, than in order to achieve what I guess you could call filmic impressionism. Clearly, the visual experience is central to "The Tree of Life," which might be why it makes so many people think of Kubrick. But the look and rhythm of Malick's film is less sharp and more dream-like, its main function appears to be to create an atmosphere, and this I think is part of why the film polarizes opinions so much. There really are no different levels here, there is one single experience. If you agree with its philosophy, then "The Tree of Life" is an intense way of viscerally experiencing thought, or of thinking in images, whichever way you want to put it. But if you do not agree, then by removing one element the whole work collapses like a house of cards, and the images are, as it were, hollowed out by their inability to point to anything beyond their own beauty. (Some people might respond that this is true of Kubrick's "2001: a space odyssey," but I would argue that that film is the translation into images of thoughts that are more ambivalent and complex, though not necessarily more serious, than the concepts meditated upon in "The Tree of Life").
Again I must repeat that this is merely a review of one aspect, not of the whole movie. If you have, as I have, read or heard that this film's visual style amounts to seeing a long-lost work of Kubrick's, I would say that such comments are based on a misconception of what the two directors use their visuals for. Both want you to look at their images very closely, and both hope that this will heighten the intensity of your experience. Both are, in that sense, not interested in realism aspiring to either objectivity or neutrality. But where Kubrick often uses his images to comment on the events he shows, Malick uses his to remove all emotional distance. Which method and which experience you prefer is of course entirely up to you, which is why my rating of three stars is merely to be understood as the closest one I could give to 2.5 - no decision either way.