There are plenty of issues with the IJS that need to be addressed, but if a skater has problems with jump technique - which, based on Nagasu's scoring in recent years, it seems she does - should that skater be rewarded as though everything was perfect? If the argument is that Nagasu's PCS should have been higher, that's okay. But UR calls and their implications are not new, and it really shouldn't have been so hard for NBC and the commentators to explain to the audience what had happened.
Here, I'll give it a shot: "Mirai Nagasu has wonderful presentation, she's an exciting skater, and she landed her jumps. However, several of the jumps she landed were not actually triples because she did not make three rotations in the air. This means that they were scored as doubles, and you can't win US Nats by doing double jumps, even if your presentation of the program is fantastic." I've heard the "marked as a double" line so many times on Eurosport, and it's not as though US commentators can't point it out, too. This is not rocket science.
p.s. why are the senior disciplines in the US referred to as championship disciplines? Are the junior and novice skaters not champions, too?