That is the feeling I had in the first act of this movie. By the second act things become a bit more conventional. The second and some of the third act become survival horror in the vein of similar Japanese stories like Resident Evil. This does not take from the compelling nature of the story and its mystery, but did not feel as rare a story experience as the first act.
The third act however, is filled with exposition that is difficult to follow and otherwise loses interest for me. At one point things become more "anime sci-fi" (a concept I simply cannot explain well), which is not a problem; expect that I didn't feel the story up to that point was building toward it. It felt less creditable for me.
The last 20 minutes, things become very muddled and subplots for the remaining survivors and their true motivations get tangled up in a more and more nonsensical plot. Things become more fanciful for the sake of animation visuals and sci-fi explanations for such events, if not ignored, seem to be quickly served out. More interesting, if you can trudge through these problems, is the ultimate twist ending involving the young female protagonist.
And my major complaint with King of Thorn, however, is that many action scenes switch from the otherwise traditional 2D anime style, to a cell shaded CGI animation process. It's 3D computer animation that is processed to look flat and try to mesh with the majority of the rest of the movie's hand drawn style. No doubt this was a cheaper way for the animation team to create complex action scenes and have more control, but the two styles do not mesh well. The cell-shaded CGI is not as glossy in color as the 2D animation and also misses many drawing details, like grime and dirt on the characters faces. Inexperienced anime viewers might not pick up on the switch all the time, but may still feel the action scenes have an odd movement and don't quite sit right.