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The Sci-fi subplot in Amulet feels kind of dislocated with the rest of the story. It's hard to describe properly, but imagine baking a cake, you wanted to add tomatoes to the cake but you forgot to add them during the mixing process, so instead you use tomato sauce as the frosting for it and now it tastes like an evil pizza because you also added cheese on top. That's like the main story and the subplot together, not the best mix.
It's probably just me but, I feel like the robots and stuff in the later books tend to feel like they're from another story. At least the early books had more of a steam punk feel in the world building and such but later it feels like advanced technology just popped out of nowhere. It feels less like a fantasy story with a few elements to make it It's own thing and more of a mess of genres from magic, to tech, to a bunch of aliens and stuff.
It feels so disorganized to me, and I'm not really the best critic but I feel like they shouldn't have even had that many Sci-fi elements in the first place. The alternate world, old robots, and steampunk like style to some parts of the story would've been enough. I don't know, I'm probably just rambling here but the Sci-fi parts just feels awkward to me, especially with the already established fantasy setting. I'm not saying that Sci-fi and Fantasy genres don't mix well, they can go well together in fact, but when you don't add the ingredients properly the final product will come out unsatisfying.
In conclusion, I feel like it was either wasted potential or nowhere near potential when it came to the Sci-fi stuff