I see this going to be the new "Vincent vs. Jason going to worlds 2017" argument 2.0. That debate lasted for like four months! A controversial decision, which I think was for the best at the time. Vincent won worlds and Jason got the third spot back.
As for today's decisions, I think was complicated. But I think the main decider was Vincent bombing his FS. If he had done well, USFS could assign him to the team event FS without much worry. Instead, it was clear his nerves are still a problem. Jason is more consistent and would at least not drop to the bottom.
According to the rules, Jason was more likely to be chosen because of his body of work and the stability of his international scores. Ilia wasn't consistent during the fall. Yes he won at the junior level, but it wasn't clean. This was his best performance. It's not uncommon for skaters to skate their very best at nationals after a mixed season.
I maybe there are other reasons under the radar. Maybe NBC wants feel good comeback story for ratings. Who know? All I know is this decision won't stop Ilia. It's the beginning of his story. Michelle Kwan was left off the Olympic team in 1994. I've always said that's one of the decisions that pushed her to be better. (The second not medaling in 1995 worlds.) So while Russia is laughing at USFS right now and a lot of people are perplexed and disappointed, maybe slowing down and letting Ilia get more experience will be a better decision in the long run.