Well you pretty much established the main reason why you think the nfl is better with your first sentence...merely because you dont have a team to go for.  With BC as pretty much the only option, I dont blame you.
Comparing the nfl to college football with parity is dumb.  College football (FBS) has 120 teams, of which about 70 are in bcs conferences.  They play 12 regular season games.  It's kinda hard to compare that to the nfl with a lot less teams and more games.
BCS does suck, but it doesn't define the sport.
Yes, it, and espn are biased toward the SEC.  it sucks.  That championship game sucked too.  you cant judge college football with one year, you can't even judge it based on the sec domination that has happened the last 6/7 or so years.
College football has tradition and soul that the nfl will never match.  Most of the time they play in stadiums that are super old with cool histories, with names like Jordan Hare, Bobby Dodd, bryant-denny, wallace wade.  In the nfl, you cant have a stadium over 30 years old (there are a couple suggestions) and they have names like bank of america stadium, sports authority field, fedex field, etc.
In the nfl, teams can leave cities, and tradition cannot be established like it is in college football.
Only a few teams in the nfl have some sort of valuable tradition.  I can find about 20 cfb teams for each of those.