Wagner did not beat Gold in the 2013 Nationals FS---Gold scored 132.49 to Wagner's 121.27, but that was just enough for Wagner to defend her title, because Wagner had won the SP with 67.57, while Gold was 9th in the SP with 54.08. There was some complaining about the result, but Wagner had been ill throughout the competition, and she had won silver at the GPF that fall, while Gold had struggled in her first GP season. There was little doubt that Wagner was a deserving US champion.
In 2009, Czisny had won the SP with 65.79, more than 5 points higher than her closest competitor, Rachel Flatt. Ashley Wagner actually won the FS with 115.00, but she was 12th in the SP with 50.28, so there was little chance of her making the podium unless the top 3 bombed. Rachel and Caroline Zhang both skated clean and scored 113.59 and 112.17. Czisny skated last and was unimpressive, with a fall and a doubled jump, but her score was boosted with huge PCS scores, and her third place 112.31 was enough for her to regain her title. Yes, there was grumbling about that result.
Just because Wagner fell and Nagasu did not doesn't mean Nagasu skated clean---she did not fully rotate her jumps. Mirai also received very high PCS scores for the same kind of performance she has been giving over the past 3-4 years: expressionless face, no connection with music or audience. Yes, Mirai is very popular with US audiences, but they are remembering her as she was as a young skater, full of excitement and promise, which she showed back then in her skating. Sadly, that is the skater they see at the end of her performances, now, but no longer while she is skating.
USFS tech teams and judges have to rate the skaters on what they do on the ice, not on their popularity with the crowd or on some need to give a 'lifetime achievement' award. To do anything else is to court controversy and invite criticism.