You make some good points, though i disagree with you. FRA had the more difficult side of the bracket. As for having fatigue playing a factor, yes it did. While Indy was up 6-0 at half against both antioch and fairview, FRA had close games at half and were keeping in there starters longer, knowing that if they put in some reserves the tide of the game could very well switch and the other team get quick goals. All 3 of the teams FRA played had a offensive threat up front, and they could all move the ball (except Dickson, really the only reason that game was close was outstanding play from the keeper), so if you think about it Indy's varsity played probably a 2 games of soccer and FRA played 3. Even though that wasnt why FRA lost the game, it was somewhat of a factor. The reason Independance beat FRA is because both teams play the same type of game, and Independence was just better at it. School size really does not have that much of an impact on the game.
Edit: As for FRA being underated, i believe they should be 2 or 3 spots higher on the rankings, but their not that underrated. The real teams that are underrated are the lower seeds in FRA's District. Teams like DCA(beat Franklin) Goodpasture(Tied CPA) Ezell Harding was a great side before their breakdown after the tie with FRA, i mean even Lipscomb, a team that hasnt been great in the past, they beat FRA and had other close games against higher ranked teams