Hmmmm, the end to the Maze Runner trilogy had some hits and misses for me. There were several very suspenseful parts, but I felt a lot of the plot was really rushed, especially the conclusion. I also thought it was hampered by the fact that Thomas chooses not to recover his memory when he's offered the option by WICKED, so he ends up jumping from crisis to crisis with no real rhyme or reason. I know there's a prequel that probably explains a lot of Thomas and Teresa's past with WICKED, so hopefully that helps explain the story a little more. There also seemed to be huge parts of the story missing, since the book introduces several new characters, then doesn't flesh them out at all.(show spoiler)
Overall, this series felt a little like the show "Lost" - it started out with an intriguing premise, but then didn't really know how to wrap up all the strange things they'd created in the world, which made the ending feel rushed and muddled. I still like it, but it does fall victim to the big "I don't know where this is going or how to wrap it up" pitfall that I think a lot of YA series encounter.