Looking at last nights BCS Championship game between Alabama & Notre Dame, it certainly did not look like #1 was playing #2. Alabama looked like they certainly belonged there; Notre Dame looked so over-matched.
That's why the play-off system is crucial if crowning a national champion is going to have a more objective process to it. Also, the selection process needs to scrutinize better Notre Dame's scheduling that does not have to negotiate a conference slate and maintaining an abundance of home and friendly site games. Not to take away from ND's fine undefeated, regular season, but that was not the #2 team in the country. TV pundits can make excuses, but it comes down to delivering or not, not background stories with flare.
Agreed on the playoff system.
But I also think that the problem starts way earlier.
1) Importance of the Conference Championship Game as a Filter:
I think the conference championship game is an important aspect as well. It's a filter or sorts, whereby the school that finished top in one division needs to play the best from the other division, many times, a school that they might not have played against. And we've even seem some strong opponents from the other division that might not be Top 10 ranked, give the higher ranked opponent from the other division a run for their money, a way to toughen them up for the Bowl game (in this case NCG). And when that lower ranked opponent upsets in the conference championship game, it removes a potential fraud from being in the NCG.
Those filters are a big help to ensure a school is prepared and more worthy of being in the NCG.
2) 1 (and some 2 loss schools) ARE Better than Some Undefeated Teams:
There is also the matter of the ranking system. For some reason, pollsters from the media to the coaches, seem to be stuck in an archaic system where they reward undefeated schools, regardless of who they have played. We have seen this forever with Big East schools ranked in the top 3 going into the final 2 weeks of the season, despite schedules that include 7 Big East games and 4 against FCS, Sun Belt, MAC schools. When a Big East team plays an average CUSA school, it's considered some sort of huge accomplishment or test.
Notre Dame's home win over Stanford in OT was their lone big win. Some might look at their wins over Michigan and MSU or even Oklahoma as huge accomplishments. They were good, don't get me wrong. But not SEC good. The SEC schools play those types of games 5 to 6 times per season in some years. Throw in a CCG over what is usually a top 7 school and it's another one. The Pac-12 has had years like that as well, when you had only 10 members and 7-8 were ranked. Big Ten certianly has had those types of years too with OSU, UM, MSU, PSU, Wis and even Purdue not that long ago (Tiller/Brees years).
Did anyone really think Notre Dame was a better school than Oregon this year? Likely not.
But back to a playoff...it does come back to that. 4 schools isn't quite enough right now but Notre Dame would have had a chance perhaps to play a school like Oregon (if at-large schools could get playoff bids in the future) with the winner moving on to a semifinal and then NCG.
So yes, a playoff system will certainly help in at least 1 way: a school will need to be battle tested in at least 1 game to reach the NCG...which Notre Dame did not have this year. SEC, Pac-12, Big Ten and ACC schools will have (2) games to get it right with the CCG and the Semi-Final (in years when each gets a team in the Playoff4)