My opinion (and it's only an opinion of course)
It was a movie cursed by being released six months after Saving Private Ryan. Where Speilberg chose to give audiences a simple story about heroism and sacrifice, interlaced with the chaos and tragidy of war, Marick chose to focus on the senseless nature of war itself. Unlike SPR, TTRL doesn't leave you with a warm and fuzzy feeling about "The Greatests Genearion."(TM)
As you mention, the cinematography stands out even to those who don't normally comment on such things. And there are parts of the movie which are captivating and sublime. However... I too don't know how to feel about the movie. Terrence Malick has an all star cast, a solid novel to work from, and a 52 million dollar budget. Given that he only makes a movie about once every seven years, I guess it shouldn't be a surprise that he stretches it out to nearly 3 hours (this is the movie that changed my mind about getting that large sprite at the theater. Oi, my bladder had about enough of that

)
To me, TTRL failed because it came across as far to preachy and self indulgent. Yes we get it; war is bad, killing is bad, taking teeth is bad. For me, I prefer to get this lesson from reading. Try Slaughterhouse Five, or Catch 22. The reason I prefer to read about how toejamty we are, is because it can set it down after reading a while, and pick it up again after I've digested for a while. I don't resent critical lessons so much when I can take them in small doses. Seeing TTRL in the theater was a gruling experience that I was not prepared for when I bought my ticket.
I'd like to give it another shot, but my Wife absolutely hated it, so there's not much chance of that
-Sikboy