The sense of wonder and discovery that made all the cruelty of the Abyss worth enduring is gone, replaced with increasingly over-the-top attempts at shock horror that crescendos with a concept so ludicrous it stops being horrifying and starts being embarrassing.
This is exactly right. The first 9 episodes of the first season of Made in Abyss represented some of the best anime of the previous decade precisely because they depicted "[t]he sense of wonder and discovery that made all the cruelty of the Abyss worth exploring..." It was a great, and haunting, adventure story. The end of season one stagnated, the movie went over the line that the first season flirted with, and the second season lost all of the qualities (other than high production values) that made season 1 memorable. The exploring was outsourced to the flashbacks of side-characters, and the whole season was stuck in a single location that was not particularly interesting.