These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Designated Hero / Designated Villain: Riddle me this. On one side, we have a 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 goes to the girl who can fix it, and asks politely. On the other side, we have a genetically engineered plant that has attained sentience and mystic powers, and decided to massacre a few billion people and ravage human civilization for reasons it has never chosen to elaborate on, and then withholds key survival necessities (notably water) from the remainder at a whim. It sees a girl who has access to the equipment that can destroy it, and A: tries to kill her repeatedly, B: demands she be given over to it while withholding water. Who sounds like the bad guy here? It's pretty clear the scriptwriters disagree with me.
Since the moon being partially destroyed and most of humanity being wiped out was Shunack's fault, however unintentionally, and since his little method of cleansing his guilt would have eventually wiped out the rest of humanity as well as the Forest, cheering for Agito becomes that much easier. Also, considering all the fuss about deforestation, pollution and climate change, portraying the destruction of forests as a good thing was probably best to be avoided.
Furthermore, most people who "ask politely" do not do so while accompanied by a bunch of walking tanks.
This troper thought that the forest was just taking its long over due revenge over the humans who mistreated it for so long.
Eh, except the forest explicitly came from the lunar terraforming experiments and not the result of any terrestrial forest, so it's been antagonistic to humans since its creation.
I think the best explanation is that, The Forest is not a malicious entity. It left the moon to grow, and Earth was the closest source of water there was. So, it beelined there as fast as possible before it would die in space. Unfortunately, their arrival at speed was basically like a worldwide meteor strike. In the intervening years, it seems, The Forest has either Hoarded or Safeguarded the last of the water in a measured attempt to stay alive. It is not heartless, otherwise it would have killed all the humans long ago. The forest is trying to balance the needs of the humans with itself, and the Forest needs a great deal more water. Whether the Forest is holding the water for it's own survival, or it is trying to reseed the Earth is another matter that isn't explored in the film.
Regardless of whether or not The Forest was Gaia's Vengeance, as far as we know, The Forest doesn't really do anything but create an area that humans cannot live in and actively does harm to them. Technically speaking, the only reason anyone really cooperates, barring a few Forest sympathizers, is because they have to. Which leads me to my point, if The Forest doesn't do anything but be a detriment why is it's continued existence so important? On another note, some of the things the "villain" does are pretty stupid/thoughtless which leads to me thinking that the writers had to shoehorn in stuff like that to justify making Shunach the antagonist
The Forest by now is an intelligent being. Based on the behavior of Ragna it has no reason to trust humans. Why should it trust that they will not destroy it if given the chance? At worst this is a battle between which intelligent lifeform dominates the planet. The Forest is trying to maintain a co-existence where both humans and the Forest can survive, but it will not risk its own survival by placing its faith in a race that has proven it cannot be trusted or that would tolerate another species not bowing to it.
Marty Stu: There is a strong case for Agito being one, one of the biggest bits of evidence being the above entry for Boring Invincible Hero - there is literally nothing that harms Agito. Except some sleeping pellets, but under the circumstances that's like throwing tranquilizer darts at a living nuclear bomb. It'll knock it out for a bit, but will it really do much?
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.