There are two basic arguments for keeping the BCS as it is, or at least similar to the current arrangement. The first is that under the current system, half of the teams that had a good year end the season with a win. That is very important to the fans and for recruiting, and therefore, the schools like it. Under a 16 team playoff system, 15 of the top teams would end the season with a loss. The second argument is that a playoff system determines which team peaks at the end of the season, and allows 16 (or 32, or 64) teams to see which one has survived the season healthy enough to continue through a slugfest of a playoff and get the right breaks at the right time. The BCS pits the best 2 teams against each other in a 1 game, 2 team playoff with winner take all. It's not really about who is able to peak during the long playoff month or two, but who can gear up for a single game with several weeks off to heal and prepare. It's a different goal, and it's what has been going on for over 50 years at this level of college football, and creates a different result than a playoff system. Not necessarily a worse result, just different one.
The chaos of the bowl games prior to the BCS sucked. Right before they instituted the pre-BCS system, bowls were sending out invitations before the last games had been played and often ended up with real stinkers because the top 10 team they had invited lost their last big matchup against thier biggest rival. And it was often impossible to match up even top 5 teams for what would be the national championshi game. For instance, the 1983 season had 4 top teams in Nebraska, Texas, Auburn, and Georgia. They were the only teams in the nation with either 0 or 1 loss, Georgia had only lost to Auburn and Auburn had only lost to Texas, while Texas and Nebraska were the undefeated teams. But there was not mechanism for Texas and Nebraska to play due to the conference tie-ins. Texas got a great matchup with Georgia as a consolation and Nebraska was locked into the Orange Bowl and fell to playing a 2 loss independent Miami team. The rest is history and Miami won their first MNC over 4 teams with 1 loss. Auburn had a less starstruck matchup in their bowl and even though they won, they weren't considered for the MNC title over a two loss Miami team that got to play at home in against a huge Nebraska team that had racked up 60 points a game all season, but couldn't make the Option attack click after a month of rest.
If you ask me, I'll take the current system over that any day, but it would be nice to see maybe a 4 team playoff under the current system with the 4 BCS bowl determining which 2 teams met for one more game in the final. This would allow for the exact same schedule we are running now, lots of bowl game trips and TV coverage for all of the wannabes, and a little less controversy over which top 4 team got left out. But someone will always be on the bubble and not make it and you'll never get rid of the controversy.