The biggest difference I find from this manga ver vs novel ver:
The MC personality
This is too much difference, like watching 2 different person in the same situation. In the novel, MC is in the same situation, but handle it differently.
MC in the novel just born recently, but has so much blank memory & jumbled information from modern era (guns, plants, human nature, civilization, etc) and from that has wisdom. He doesn't swayed easily nor quick to panic, he's smart, calm, composed, and reassuring. He wouldn't flinch from just some threat, he will threat them back many folds. Show his power when it's needed, but not abuse it. A perfect leader worthy of the wisdom & information he has.
MC in the manga, boy oh boy, he's just a kid. Just some average highschool boy with some power & 1 pages google search result as a information source of his innate memory. He knows it, but can't use it skillfully. He even got played and almost used by a goddamn human merchant. Not a single piece of wisdom & charisma as a leader, I even think his monsters follow him just because he made them, not because any other feelings like sympathy nor share the same vision & ambition. He talks big about living in harmony & compassion with human, but scared of them consistently. I wont even surprised to see him 'eaten' by his power alone. His medal power is so much stronger than his mind capability to handle.
Thats why I pity you all, the 'only manga' reader, to see this awful version of MC. I beg you, please, please, please read the novel version. And you will see how badass this story (especially the MC) truly can be.