I just watched the movie and I have to say everybody missed the plot of the story, you are wrong if you think the synopsis is a spoiler.
Spoiler for Sky Crawlers plot:
There is nothing about war or planes or pilots in WW2, there's no clones and nobody is immortal or eternally young...It is not a sci-fi movie.
Everything is symbolism in this movie. The dogfights are just pretext to illustrate the struggle of children or teenagers growing up into adult world. I don't know if you noticed but the main characters are children and their parents are there too, Mama is the kids mother, the military General who prevent Kusanagi from passing a gate is her father, it looks like a scene when a girl is introducing her boyfriend to her parents.
Yuichi lives in a kid's room and has bunk bed. He goes to a restaurant runned by a couple who are actually his parents. There is an old man outside , probably his grandfather and probably dead, but i'm not sure about why they focused on him.
During the dogfights they speak english, because they are in the adults area they have to adapt to adult language.
Ultimately to become an adult the kid will have to kill the image of his father, he can't kill him but he has to confront him , when it's done the kid dies and lets the place to an adult.
At the end there is another boy, it could mean their parents had another children or it could be Yuichi's son. Yuchi managed to go into the adult world while Kusanagi seems to be stuck in childhood.
My too cents.