I think that USFSA was tired of hearing all the crap about how its only the "baby ballerinas" that win. They wanted a mature, polished woman who everybody has a soft spot for.
I honestly can't figure out exactly why they favored Alissa over Caroline. Rachael I can maybe understand, because she doesn't have that star quality nor amazing non-jumping elements, her programs have been so zzzzzzzzzzzzzz this season, and even her 3-3 has been MIA lately. With Caroline, maybe it's a combination of different reasons, as different people have been proposing:
-- USFSA wanting to have a more mature, womanly national champion (after the extreme hyping of Mirai at National's last year, she blazed out with her growth spurt, not saying she won't make a comeback like Phaneuf or even better, but it shows the danger of placing too much bets on a young teenager to be the future star)
-- the momentum Alissa carried into the LP with her shockingly clean SP (that is so rare for *her*) and Brian Boitano telling the media repeatedly how much she's improved this season; many have been waiting for years for Alissa to go clean, and she started off this season well, skated a great SP, so it really seemed like this just might be the year for her to shine, and so the judges gave it to her despite her less-than-impressive LP
-- the downgrades and edge calls Caroline got slapped with when she entered the senior ranks, just as those tough new penalties were coming into play, made people worry that her future is doomed under this system (which is obviously an exaggeration considering she got the highest TES here despite not having her 3F-3T's ratified)
-- all the high expectations surrounding Caroline before she even entered senior ranks turned into frustration/impatience or even disgust when she didn't immediately turn into a senior star (related to the previous point)
In any case, whatever the reasons, to me it seemed unfair bias was clearly there at National's in the judging of these two young ladies. One can argue about where that bias came from or what future expectations were involved (like who has higher scoring potential at World's). But in any case, if figure skating is going to be taken as a serious sport, its judging should be based on *only* how the skaters execute on the night, not on past history or future potential. That is just plain ridiculous.
I was so angry after National's I felt like I didn't want to watch skating again... I would watch JW and skip WC as a protest, except it would hurt no one but myself.

I want to cheer on Mao Asada and Laura Lepisto, among others.