My brother and I went on rants together on what we hated about the movie once...
The two issues that came up immediately were how the Grievers and Theresa were handled. The Grievers, if you remember how they were described in the book, were these big, slimy monstrosities conjoined with machine... they looked like slugs with patches of hair on their bodies, and they had mechanical limbs sticking out of their backs. Said limbs had nasty bits like pincers, buzzsaws, and the like attached. They could curl into balls, spikes would protrude from their bodes, and they could become a whirling ball of death.
Reading the books, they sounded grotesque, misshapen, and terrifying. What the movies gave us instead... was some generic CGI beast with spider limbs and sharp teeth. Are you kidding me.
Aaand then there's Theresa. In the books, she had a pretty big role. Aside from being the harbinger of the end times, she also had this telepathic link to the main character, Thomas, and there was quite a bit of interaction between the two. She was a major player. In the movie, not only is the telepathy gone, but Theresa's just... there. She doesn't DO anything! She's just this random token female who could easily be killed or replaced by a random guy, and it would have no impact on the story whatsoever. What's worse is that quite a bit of the conflict in The Scorch Trials is built around the relationship between Theresa and Thomas (mostly straining it with apparent betrayal and breaking off the telepathy), but since the movies don't have that relationship in the first place, it's going to end up looking phoned-in and weird that Thomas is worried about this chick disappearing.
By itself, the movie was alright, I guess. It's not horrible. But compared to the book, it hardly does its source material justice. The stuff that made the book stand out to me- the suspense, the uneasiness, the mystery- weren't captured very well in the movie, and as a result, the movie ended up looking like a generic YA adaptation. Because it was.
God help us with the next installments. At least the Grievers, even if they were kind of butchered, were novel in concept... now we've got Cranks, which are basically zombies. Sigh...