While alot can change in 2 years looking ahead to Sochi it seems right now the 4 favorites for the 3 spots (if the U.S even has 3 spots) would be Gracie Gold, Wagner, Czisny, and Agnes. The second tier contenders with a lesser shot of sneaking and making it would be Nagasu, Zhang, and possibly a couple of the current top juniors. Flatt I would put behind even that group, maybe on par with someone like Christina Gao, but even Gao is far more likely to improve between now and then. Frankly I think her making the team for Sochi if she continued would be a miracle, especialy as it would take a 110% effort on her part to even get back up with a fighting chance and I cant see her giving that now.
Also note IF the U.S has 3 spots all that means means their top women are finally doing well (which they werent while a much stronger Flatt was one of the their top 2 or 3), which doesnt make it any more likely a past her prime Flatt who is no longer a USFSA favorite could even hope to make it.
As for saying she could have skated better this year at Nationals, well yeah but that goes for almost anyone. Czisny made more mistakes and left out as many things as she did and finished 2nd. Agnes bombed the long badly and won the bronze. Nagasu was about 40% of her potential, had I think 1 clean triple in the long, (discounting the end of a combination where she fell on a double) and nearly tied Rachel. Wagner even made one major mistake and alot of minor ones in the long program. It is not like she had a worse competition than most. As only a part time skater the long is about the best you will see from her anyway. I dont think you will see 6 or 7 triple long programs unless she is giving it 110% again, which would likely mean dropping school for awhile, and that isnt going to happen.
Flatt btw is NOT Debi Thomas. Debi Thomas was an incredible natural talent so was able to get by with less total dediction than others. Flatt is not, her strength was always her determination, mental toughness, and hard work. Debi Thomas was also one of the very elite of her sport at the time. Flatt never was. Not to mention those years were Thomas's physical prime and skating peak years, kind of like what 2008-2010 were for Flatt. I would bet money that Thomas wouldnt have made the 92 Olympic team (the hypothetical equivalent for her of Flatt in 2014) as a part time student, and that despite that she is a far stronger and more gifted skater than Flatt, who had never fallen out of favor of the USFSA.