Adaptation Displacement: To many a casual Studio Ghibli fan, it's fairly unknown that there even is a manga of Nausicaä, much less that it was made by Miyazaki himself. Although the movie is really just a 2-hour compression of the first quarter of the manga. It helps that the manga was very rarely printed.
Anvilicious: Of the Green Aesop variety, mostly for the film though. It gets a bit more complicated, if not somewhat subverted towards the end of the manga. Specifically, the question of whether or not the Master Computer's plan to artificially restore Earth's old ecology is just as bad as the callous environmental destruction that preceded it, since it would mean the deaths of the countless biotechnological creatures (including "Humans") who have made a life for themselves in the new world.
Nausicaä herself is much colder and more dire than in the movie, fitting for the manga's more nihilistic tone, although she still ends up largely on the side of idealism. The fact that her real opponents in the manga are full-blown Omnicidal Maniacs, Master Computers and whatnot means she also needs to have a little more steel in her will than her film counterpart ever has to muster.
Despite being uncut and more accurate, Disney's dub of Nausicaä still has its share of harsh detractors, with some declaring that it still fails to do justice to the original Japanese. You'll have to decide for yourself if you like it or not.
Fans tend to be split over the manga. Some consider it to be a vastly superior story to the movie; others think the plot gets too muddled and self-indulgent in the later volumes and prefer the movie's Adaptation Distillation.
Escapist Character: Nausicaä. Who wouldn't want to fly around the world in a miniature aircraft, exploring beautiful forbidden lands?
Jerkass Woobie: Possibly a number of characters, but perhaps most notably Kushana. Introduced in the film version as a seemingly stereotypical evil queen ("Nice valley. Think I'll keep it."), her status as an apparent Card-Carrying Villain is quickly subverted. This apparently was deliberate on Miyazaki's part — he describes Nausicaä and Kushana as "two sides of the same coin", largely differing in that Kushana has "deep, physical wounds".
Les Yay: In the manga, Nausicaä and Kushana have some of this going for them as Kushana seems to take a bit of a shine to Nausicaä as the story progresses.
Macekre: Warriors of the Wind again. The incident is why all Studio Ghibli licenses contractually require that not a frame of animation be altered or cut (with the obvious exception of translating the credits).
Moral Event Horizon: In the movie, the Torumekians (especially Kushana and Kurotowa) crossed it early on when they enslaved Pejite and assassinated King Jhil. However, the moment that seals them as barbaric and irredeemable warmongers is the invasion of the Peijite aircraft which was filled with children and the words that followed it:
"Leave no survivors!"
The Pejiteans themselves cross this line when they reveal that they intend to bait the insects into the Valley to wipe out the Torumekians there and wrestle back control of the Giant Warrior, an act that would also kill all of Nausicaä's people. Played with however, as it's the Pejite leadership that wishes to see this plan through while the civilians, with Asbel's help elect to free Nausicaä rather then to be responsible for genocide.
The manga, full as it is of Gray and Grey Morality, doesn't have nearly as much of this, but there are a couple moments. For instance, when the Doroks are revealed to be manufacturing toxic mold to use its miasma to slaughter the invading Torumekian troops Ė Charuka pulls his HeelĖFace Turn once he realizes how insane that plan is.
Narm: Nausicaä's (pink) dress is soaked with Ohmu blood in the film and causes it to turn blue, and some earlier shots depict it as being soaked with Ohmu blood and starting to change colour slightly. However, it suddenly turns entirely blue in practically one frame - and the blood had apparently been so soaked it got her entire dress, yet none of it got on her skin or her hair. The fact that, despite the Ohmu blood soaking her clothes that fully, the logo on the front of her dress is still there.
Squick: Film-only example. When Kushana takes off her glove to show that she no longer has an arm and then says "Whatever lucky man becomes my husband shall see far worse than that." Ew.
She retains the armor on both her legs after taking off her armor, too.
Note that in the original manga, Kushana appears to be 100% whole (she retains her arms and legs in any case).
Word of Miyazaki states that Nausicaä's resurrection near the end of the movie was not meant to be analogous to Jesus and that he would have changed it if somebody had pointed out the similarities before the film came out — Miyazaki is many things, religious is not one of them. This may well explain some of the open discussion about the permanence of death (and how ways of avoiding it are explicitly unnatural) in later stages of the manga.