It's deeply Catholic message about sex + relationships
...That, as far as I can tell, all critics are failing completely to engage with, with the exception of Christianity Today. Which is silly; this is one of the morally driven films I have ever seen.
Yes, it is a poem, and in my viewing, a beautiful one. I have never seen a film so steeped in how lovers touch one another. It's lyricism is its animating force, not its message, but its message is none-the-less overwhelmingly clear:
When Marina leaves, Neil's relationship with Jane is summed up by her in starkly Devout terms: "you turned it into nothing, into lust and pleasure." He has previously said that he lacks faith.
Marina returns. There is the scene in the doctors office, and after this, for the first time in the entire film, we see them naked together in bed. Although obviously the characters have been having sex before this, the filmmaker has focused on their rhapsodic clothed foreplay. But now they are in bed, and he seems hesitant, and she says to him, "what are you afraid of?" In terms of a momentum of imagery, this is clearly associating sex with procreation.
Right after this, she cheats, and following the fight at the burger joint/freeway, we suddenly see her with an infant. The Priest's sermon comes to mind, in which he talks about Love as an act of surrender as much as an act of passion or emotion. After some more fighting, Neil bows down to her, not in the way he has before, which has usually been as a sensual act, but instead holds the static bow, an almost ritual act, a literal act of surrender. Then the imagery loops back to Mont St. Michel, and we see the two of them, presumably years later, in a home with two children, both much younger than Tatiana, so presumably their two children. The Priests' questioning of his vocation is resolved in the hypnotic prayer that winds up the film: Christ above me, Christ below me, Christ on my left, etc."
So for all those who are claiming that the film lacks focus or meaning, I would suggest while it may meander, it's message is unusually clear for a Malick film: love is about surrender. Marina and Neil are imprisoned by their freedom (witness Marina's friends absurd monologue about how she should play the field because she is young and beautiful); they are imprisoned by the presence of seemingly infinite choice just as the Priest is imprisoned by the absence of choice. Ultimately, in order to be free of their existential prison, they must surrender to each other, to their loving but imperfect relationship, get married, have children. Thus the film is both a celebration of romantic love and a very Catholic critique of it. "Why do we come down?" is the recurring phrase in Marina's monologues. We come down when we expect Love to be something it cannot be. Commitment is not about finding the One who will keep up you Up There (on top of the mountain, in terms of the films' early imagery), but is inevitably about sacrifice and surrender, and, yes, about making children, which is perhaps the most pure form of sacrifice and surrender that there is.