Idiot Plot: Much of the plot revolves around the supposed heroes being colossally stupid. This is pointed out repeatedly within the story itself.
Moral Event Horizon: A major theme of the story is regarding GLaDOS's Moral Event Horizon. Though for many readers, she has passed it early on when she puts Fluttershy in a coma, Celestia explains in chapter 20 that her true Moral Event Horizon corresponds with her Despair Event Horizon.
Sequelitis: While good, it lacks the humor of the original story, and while the story is more complex, it is much more obviously a fanfiction-style plot compared to the original's simpler, more faithful story.
Unintentionally Unsympathetic: The fic makes an attempt to portray GLaDOS in a sympathetic light, revealing Caroline was an unwilling participant in creating her, and implying that GLaDOS is secretly a sad and lonely Stepford Snarker. As Twilight points out though, it's hard to show any sympathy for her after she set fire to the Everfree Forest with purposeful intent to try and get Fluttershy killed, not to mention her actions in the original story and first two games. Especially since if anyone would try to show GLaDOS friendship and kindness, it would be Fluttershy.