Director Mamoru Oshii is one of the stranger Anime directors out there ... although he stands out for being weirdly contemplative in his movies rather than weird random violence (which is common enough in Anime). I love and adore both "Ghost in the Shell" and "Ghost in the Shell 2: Innocence," both subject to his odd moving meditation moments. These moments can even be found in his earlier "Patlabor: The Movie" which I saw relatively recently. "The Sky Crawlers" was filmed in 2008, four years after the second GitS movie. The moments of contemplation are somewhat better integrated into the story line, but it's still clearly an Oshii movie.
Our protagonist is Yūichi Kannami (voiced by Ryō Kase), a young pilot newly assigned to Area 262 (as this fetishizes aircraft, that may be a reference to the Messerschmitt Me 262). He gets an oddly lukewarm reception. He rapidly proves to be a good pilot, and his room-mate takes him out on the town where he meets the prostitute Fūko. But even as that relationship starts, he finds himself entering a relationship with his commanding officer, the homicidal and/or suicidal Kusanagi. (Anyone familiar with "Ghost in the Shell" will remember that name.)
As this proceeds, we're also finding out that all the pilots are "Kildren," humans who never grow old ("why would we want to grow old when we could die any day?"). My guess was that the name was a play on "Children" and "Kill." Wikipedia tells me that the Japanese term was "Kill-dolls," which is even grimmer. We also learn that the people we're watching work for Rostock, which is perpetually at war with another company called Lautern.
There are a couple blatant references to GitS: the Base CO's name is Kusanagi, and there's a basset hound who lives with them at the base and is in a lot of shots. I don't know if "Kusanagi" is a common Japanese name ... I don't think so, and even if it is I don't think he should have repeated it here, particularly not as a female leader. Even if it's their equivalent of "Smith" as a family name.
As usual for Anime, the point of the story is a bit muddy. Even though one of the main characters moralizes a good bit of the punchline out loud at one point, ie. the general populace is so used to war that the only way to maintain peace is to create a controlled constant war. But what they were trying to say with the creation of "Kill-dolls" and their never-ending horrific lives was never clear to me. Not a bad film, but nowhere close to GitS.