All that needed to happen for the Ducks to pass FSU after last week was for Missouri—who was ranked ahead of the Oregon in many computer systems—to lose. That loss combined with Oregon's win over a highly-ranked UCLA team catapulted the Ducks to a comfortable lead over the Seminoles in the latest BCS standings.
Long-term there is little chance for Florida State to pass an unbeaten Oregon team that simply started ahead of the Noles in the preseason rankings and has given voters little reason to move it down in the rankings. And despite all the discussion about computers and strength of schedule, the polls are really all that matters in the BCS formula.
After a 2003-04 season in which a USC team ranked first in both the AP and Coaches' polls did not make the BCS championship game, the impact of the computers was reduced to near insignificance, making sure to weight the system such that the top two teams in prior years' polls would always have made the title game.
That the top two teams in the polls has gone to the title game ever since is thus no accident, as the polls account for 2/3 of the BCS formula, meaning that if a team is second in the polls, there would have to be a substantial gap in the computers between that team and the third-ranked team.
But because the computers cannot take margin of victory into account, undefeated teams inevitably rise to the top of the computers by the end of the season, meaning an unbeaten Oregon would be no worse than third in the computers given its obvious schedule edge over Ohio State.
As a result, even if Florida State were ranked first in the computers, it is highly unlikely to be enough to overcome the other 2/3 of the formula, which would presumably still have Oregon ahead of the Seminoles.
Fortunately for the Seminoles, the season doesn't end today. There's still a lot of football left to be played, and it seems this sort of hand-wringing has happened every year in the BCS, only to be settled as upsets and the unpredictable nature of college football takes care of setting up a satisfying title game.
Only once has an undefeated major-conference team been left out of the national title game: Auburn in 2004, two years before the SEC began its unprecedented run of seven straight national championships. The fact that only two of those seven champions (2009 Alabama, 2010 Auburn) finished the regular season undefeated should be taken as a testament to how rarely multiple teams from major conferences finish unbeaten.
Evaluating the Schedules
The real discussion therefore concerns the likelihood of each of the top three teams going unbeaten. Below are estimates of the likelihood of each team going undefeated, using last week's F/+ rankings (since this week's are not yet released) as a baseline for estimating win probabilities and then adjusting for matchups.
I happen to think LSU is a bad matchup for Alabama this year due to the matchups between the Tigers' outstanding defensive tackles and Bama's interior offensive line and LSU's receivers against Bama's secondary. But there's little doubt that if Alabama gets past the Tigers, they're very likely to go unbeaten the rest of the way, though Auburn has the potential to pull an upset in a rivalry game at home.
Oregon, on the other hand, is actually more likely to lose than to go unbeaten. Surprisingly, last week's F/+ rankings actually favor Stanford over Oregon despite the Cardinal's loss at Utah. Even bumping that to a toss-up game only brings Oregon's odds of going unbeaten to around 24%. If the Ducks do make it through that game unbeaten, their unbeaten probability raises to approximately 45%, meaning they're still more likely to drop a game over the course of a very difficult schedule down the stretch.
Unlike Oregon, the Noles are actually more likely to win out than to lose a game, even when accounting for compound probabilities. Miami is not really one of the best ten teams in the country and matches up poorly against Florida State. Florida is a shell of itself after a rash of injuries that has helped make up for the good fortune the Gators enjoyed in 2012.
All told, given the above scenario, despite the fact that an undefeated Oregon would almost certainly go to the national title game over Florida State, an Alabama-Florida State matchup is actually the most likely scenario at this point in the season, with that matchup about 25% likely based on my adjusted probabilities above. At any rate, the next two weeks, in which FSU hosts Miami, Bama hosts LSU, and Oregon travels to Stanford, will certainly clear the picture significantly.