Speaking of songs from the movie; the ending piece "Ai no Melody" (lit. "Melody of Love") is a beautiful, glorious mix of awesome which manages to be both a Crowning Music of Heartwarmingand a Tear Jerker.
Designated Hero: We're supposedly supposed to root for the Forest in this, but it's pretty hard to do that when the Forest is hostile to most living things and actively withholds water from the humans to get what it wants. That's on top of the fact that it took over the planet and collapsed civilization, forcing those that remain to either work with it or become desert dwellers.
Designated Villain: On the other side, we have a Well-Intentioned Extremist scientist who, in his impatience, screwed the world. He tried living in the world as it became, and eventually decided it was absolutely unacceptable. So he intends to use the E.S.T.O.C. to destroy his creation which, as noted, is not exactly cooperative to those that don't flat-out obey its whims. Yes, this will be rather harmful to the civilization that exists now, but even the scientist who built the thing acknowledges that in a recording and still thought it was worth leaving the option.
Science Is Bad: Generally seems to be the case. Genetic tampering led to plants destroying the world and the creation of volcanic superweapons. Toola discarding her future necklace phone at the end is portrayed as a good thing. Then again the wise plants are indicated to be good, and they are the product of science too.
Any "technology is bad" message is undermined by the fact that Neutral City citizens are reliant on mining equipment and use old world supplies and Ragna can only survive in the desert thanks to water-extraction technology, suggesting there are legitimate uses of technology. Makes you wonder if Toola throwing away her communicator was the best idea.