I've heard the arguments for:
1. Alabama was the best team (no doubt)
2. It was a defensive battle. (debatable)
3. We have to protect the regular season. (we didn't)
Here are the arguments against:
1. It's ridiculous to try and determine your championship over a month after the regular season with no games in between.
Only in D-1A College football is this acceptable. OF COURSE the game was sloppy, neither team had played a down in over 30 days. At least under the old system the bowl games were better and everything was over on New Year's Day. (Remember that? Hard to believe those were the good ol' days) At least under the old system you could relocate every TV in your house to the living room (or borrow TV's from your neighbors) and then get sick trying to watch 4 games at once. You also knew that, when this was all over, you could focus totally on the NFL playoffs. You can't say that today.
2. The B(c)S polling is a sham.
When Nick Saban (who had a definite skin in the game) voted his main competition fourth in his final poll, arguably pushing them out of the game and placing his team in, then you know this whole thing is a joke. Never mind that there's no bigger joke in College Football than the Coaches Poll (the Harris poll being the second biggest joke) but it's gotten to the point that they're not even pretending to be straight any longer. The main argument for the B(c)S is that it gives us "number one vs. number two", except that in this case, it didn't. (this is independent of the argument that Alabama was the best team.)
3. The regular season doesn't matter any longer.
One of the arguments for the B(c)S is that it protects the integrity of the regular season, a regular season that many (including me) believe to be among the best in sport. Regular season games in College Football "MATTERS" dammit. At least, that's what we're led to believe. The problem with this argument is that, in this case, it didn't matter one iota. Lest you forget, during the sacred regular season, Alabama LOST...AT HOME, to LSU. They lost and they still ended up in the National Championship Game, despite not winning their own conference. In short, the regular season matters, except then the B(c)S (and ESPN, which feeds the beast) decide it doesn't.
It's not that college football will cease to be watched because Alabama won a championship, that's not the point here. The point is that the system is gamed, broken and produced, for the most part, a bevvy of un-watchable dreck that's far worse than what the old system put out, with just as much controversy, and far less excitement on New Year's Day.
Death to the B(c)S!!! (Roll Tide*)
*Nope, not a 'Bama fan, referring instead to a certain commercial. Congrats to Saban & Co. however, they truly were the best team. Best teams don't always win the championship however. Nor should they.