It's not that the rules weren't clear--clearly, the USFSA can do what it wants when it wants and how it wants, and at some point or another the rules were announced to everyone.
That is not the problem here.
It's that neither of them are very good. (Well, by the incredibly high standards of Olympic-level figure skating, anyway. Of course, they're a lot better than 99% of those starting skating lessons will ever be.) But by skating star standards? Mediocre!
You know why you never saw the committee skipping over someone before this to put someone off the podium on the team? Because the best people actually were on the podium. They didn't have a bad day and wind up in 4th place at nationals. It would be unheard of for Michelle, Sasha, Sarah, etc. to bomb like that.
Not that Mirai is any better, as we've seen at 4 Continents. The US bronze medalist doing that poorly in a competition among lesser-known skaters? Never would've happened 10, 15 years ago.
And I'm not letting Gracie off easily, either. The national champion doing so poorly on the Grand Prix circuit that she didn't even make the finale? Not likely back in the day!
What you have now are a bunch of skaters who are inconsistent and unless a real star emerges, there will be a controversy every year as they compare each skater's good days and bad days, as everyone cries politics, racism or whatever.