^ You've articulated the argument far better than any other version I've heard or read... but I still have qualms. If the film was intended to have this clear cut, 1 to 1 nationalist message then I think it fails in certain respects. Perhaps if Anno intended the movie to carry this message his desire to also make it a cracking monster movie with all the required twists and turns sabotaged those intentions somewhat?
If the film wants to valorize the military and encourage military expansion why isn't military force capable of anything meaningful? The heroes are more like Joe Brody in Godzilla '14: bomb disposal instead of bomb throwing. There's also the heroism and out-of-nowhere wisdom of the elderly replacement prime minister, which puzzles me more than anything else in the film. The old German lady criticizing her young associates for, essentially, nationalist reservations and Rando responding in kind by sharing all the supposedly precious Godzilla information with the world. The entire character of Ogashira, who seems to exist only as a fairly simple condemnation of sexism and is made memorable by the actress. If Anno wants to end the movie with this statement about a new stronger Japan why does he pull the rug out at the end? The surprise last shot of the film gives us the impression that everything Yaguchi and the rest accomplished is all for naught and the world is still screwed. It reminds me of the end of one of John Carpenter's 'apocalypse' movies, or even the end of Friday the 13th with Jason springing from the lake. The movie ends giving you the impression that there's not going to be a Japan pretty soon, much less a new, stronger Japan. There isn't going to be an anywhere very soon.
I get the impression that Hideaki Anno... doesn't really care. I mean, he's more preoccupied with his pet themes of problem solving and self determination than he is with any moral stance or belief and is kind of clueless, and maybe too emotionally stunted to actually form a coherent political thought beyond that of a middle schooler. If he did turn out a cogent piece of nationalist propaganda he must've done so by accident, because I don't think it within his capabilities to do so intentionally.
... jeez, I got kinda mean about Anno there. I do like the film!