The BCS sucks for reasons that you fail to mention. But let's start with what you did mention. For starters, Texas A&M's schedule isn't that tough when you think about it, especially compared to teams like Iowa (who played Ohio State, Michigan State, Wisconsin, Penn State, and Arizona) or Oregon State (who plays Stanford, Oregon, TCU, Arizona, and Boise State, all teams that when Oregon State played/plays them were/are ranked in the top 10). Plus, you can't forget about the "other" games on Texas A&M's schedule, you know, against Stephen F. Austin, Florida International, Louisiana Tech, and Kansas (currently one of the worst BCS schools).
To take that a little further, how does Boise State losing on a missed FG "show their true colors", especially since they are one of the few teams in all of college that teams WON'T schedule?
But the reason why the BCS sucks, is because it weighs a conference schedule more than a non-conference schedule, which basically allows teams to schedule weak non-conference games. Also, its about popularity. If Boise State hadn't lost this weekened, Stanford would more than likely be left out of the BCS, not because they aren't a good team, but because they don't have a big enough fanbase, which BCS officals were afraid that nobody would watch Stanford, and that Stanford wouldn't be able to bring enough fans with them.
A system becomes truly sad when you start deciding to ignore good teams simply based their fanbase isn't big enough.