I was maybe 10% into this book, and was having a conversation with a teenager about this series and my problems with it, when I had a realization: I don't trust the author.
When an author's setting up a big reveal, there need to be enough clues about what's happening to keep the reader from giving up before the reveal is shown. We the readers need to twist that the author knows what they're doing, that the payoff's gonna be worth the trouble. And that's where this whole series fails. There's no sense of, well, of sense. Dashner keeps saying, "Trust me, I know what I'm doing. Just trust me, trust me. It'll all make sense." But two books in, and it's all still "Trust me! You don't understand, but you will!" The cards are too close to your chest, Dashner. I'm not willing to suspend disbelief this long.