I think I will miss the BCS. Before the BCS, #1 hardly ever met #2 at the end, so the sports media had alot more power in determining who they wanted to be national champions. This usually favored the Big Ten or Notre Dame. They could play lesser bowl opponents and still be crowned champs by the media.
The BCS ended that. The media still had some say, but it was a far more transparent process, so their role was greatly diminished. They would have loved for Ohio State to not have to play Florida in 2006 and just crowned them champs with a win over a weak Pac 10 team in the Rose Bowl, but they couldn't do it. Likewise, an unbeaten Notre Dame had to play a 1 loss Alabama team last year rather than some weaker opponent, which would have happened before the BCS. I think the BCS ultimately got it right every year, save 2004.
Now we go to a playoff, which the media has been clamoring for, because it gives them alot of power back, since they will influence more teams' chances (and since it is more of a judgement call as to who is 3-4 vs. who is 1-2). Sure the same unbeaten BCS conference teams will get in at the top, but now the media may be able to get their 2 loss USC or 1 loss Michigan in there too, if possible. There's far more wiggle room to give preferential treatment to schools in bigger media markets or simply those the more influential sports media members prefer. And as the playoffs inevitably expand, that influence will inevitably grow.
Of course, I guess the hope is that the playoff format and the concept of more teams "settling it on the field" will lead to a somewhat more decisive champion (though, like I said before, I feel like the BCS has gotten it right pretty much every year, so I am not sure how much better it can be). But playoffs have their own set of challenges. They don't necessarily decide the best team so much as the team that is playing best at the end. Were the Ravens really the best team in the NFL last year or did they get hot at the right time? There are lots of ways to determine a champion. In the English Premier League there are no playoffs, it's purely based on your record over the course of the season, so it judges the sum total of your accomplishments and failures. I think many methods are valid and all methods are debatable. There is no perfect method. I do wonder how the playoff format (which will almost certainly be expanded to more games in the future) will benefit, say a team in the Big Ten who has played a weak regular season and may have fewer injuries and better rested players for a 3-4 game playoff stretch at the end.