After a chaotic weekend in which many of the contenders from other conferences were upset, it's beginning to appear very likely that the BCS Title Game will feature a rematch between LSU and Alabama. (Arkansas may have something to say about that this weekend, though.) I'm against this under any circumstances, and not just because of some vague notion that "Alabama got its chance." I have two reasons: the regular season is a playoff under the current system, and you can't get a good sense of who is the best team in the nation without matching up teams from two conferences.
The first point is fairly self-explanatory. As I understand it, under the current BCS system, the regular season serves as a playoff. That means that Alabama was eliminated from contention when it lost to LSU. Another team needs to get a shot. If a playoff is instituted that includes berths for non-conference champions (and I would probably be against that, too), it would make sense for there to be rematches. However, that would be a different system than the one we have now, so it's irrelevant to the situation at hand.
More importantly, I think it's shortsighted to say that Alabama and LSU are clearly the best teams in the nation before they've been matched up against teams from other conferences. LSU, of course, has an impressive win over Oregon, but that was a long time ago it's only one game. Otherwise, all we know about these teams is based on the what they've done in the SEC against common opponents. We just don't know how they would match up against teh best of other conferences. Obviously, based on recent post-season results, there is abundant reason to believe that the best teams in the SEC are among the best in the nation. However, you just never know until you match the conference champions against each other in the post-season. In 2006, a lot of people thought that Michigan and Ohio State were the best two teams in the country and favored a rematch between the Buckeyes and Wolverines for that reason. However, better minds prevailed, and in the bowls we learned that not only were the Buckeyes not the best team in the nation, but that both teams were overrated and had built their reputations by feasting on subpar Big 10 competition. While I don't think the SEC is as weak as the Big 10, I do think it is necessary to give other conferences a shot in order to make sure each year. The BCS Title Game shouldn't feature rematches between conference foes in order to effectively weed out any bias that uncomparable competition has worked into the voting.
All of this being the case, I hope that voters influence the system by heavily voting against a rematch.