Author Existence Failure: Bobmin has announced that it is unlikely that he will be able to finish the third book due to contracting lung cancer.
Draco in Leather Pants / Ron the Death Eater: surprisingly averts both. While Draco Malfoy (and a couple other Slytherins) does become one of the good guys, there is a good reason for why he changes sides, and he does not become close friends with Harry. Also, Ron and Ginny do get angry with Harry and Hermione over the fact that they Impress, but Ron eventually does apologize.
Values Dissonance: Alejandro Croaker, the Head of the Department of Mysteries, is continuously hit on the head with the fact that Harry, one of Britain's few mages (wizards with power several orders of magnitude above the rest), barely wants to have anything to do with the magical world.
The Riders realize this relatively soon, as now those who were their friends don't understand the changes the Riders undergo when they Impress. Also, the nature of relationships in Pern more or less bleeds through, and there are several threesomes formed between Riders.