Fridge Horror: Schunack talks of "wiping the slate clean" in regards to humanity and keeps a firm hold on Toola even after she has served her purpose with the Ragan. It is frightful to consider what he planned to do to her after he killed all the other humans. Was he planning on repopulating it?
Intended Audience Reaction: Toola and Schunack are the only characters from the past, and thus have much more in common with real life viewers than other characters. Their bafflement, sorrow, disgust etc. for the setting is likely to be what audience reaction would be. Agreement with the later, even though he is the Big Bad, is intended so one can see how, in this hypothetical situation, he can be mistaken.
Moral Event Horizon: At first, Shunack may appear to be a Well-Intentioned Extremist and some people could sympathize (or even agree) with his ideal of bringing back the old civilization and his desire to undo his mistakes, even though it means destroying the Forest. Then he reveals that he intends to use E.S.T.O.C. to destroy Neutral City as well, simply out of spite. That decision shows that he has jumped off the slippery slope, no matter how much well-intentioned he used to be.
Science Is Bad: While this seems to be the case, given what happened in the film's backstory, it is not really the case at all.
Genetic tampering led to plants destroying the world but this was due to one person's impatience in overstimulating the genes involved.
Science led to the creation of a volcanic superweapon but the danger of this weapon is acknowledged by its creator, which is why he put in so many safeguards to prevent its misuse.
Toola discarding her future necklace phone at the end is portrayed as a good thing because it is symbolic of her letting go of her past and embracing her new life. The fact that the necklace is high-tech is incidental.
The wise plants are indicated to be good, and they are the product of science too.
Furthermore, 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.
Uncanny Valley: The twin forest spirits intentionally fall into this. They are basically Fair Folk, after all. Their attempts at mimicking human appearance and behavior is going to be spotty.