I like the concept and the detailed game design document. My main concern is the scope, especially since this is a narrative-heavy game. I recommend finalizing the main story and gameplay flow as early as possible, and consider scaling back some ideas if time becomes an issue.
Just a quick thought (not fully developed): what if the seed (the invasive species) were actually "alive" and gradually formed a close bond with the player? This could create a compelling moral dilemma at the end of the game: should the player save the ecosystem by destroying their friend, or be unable to resist their emotional attachment and allow the invasive species to continue spreading? I think this could help reinforce the idea that environmental conservation often involves difficult personal sacrifices and that choosing between personal emotions and the greater good is rarely easy.