Arguably these were merely isolated "down" years of the Pac-10, Big Ten, and ACC, respectively. The problem is that the BIG EAST of 2005 is still a relatively unproven commodity in terms of annual track record. Let's look at the BIG EAST teams that theoretically would have been eligible for an at-large berth to the BCS and/or played in a "BCS" bowl in the last twenty-five years...
Louisville: 1990(?) and 2004
Syracuse: 1987, 1992
West Virginia: 1982, 1988, 1993
(well in the last twenty years). Louisville probably would have been "Top 12" in 1990 as it was this year.
How about more "isolated down years" by other 3-loss BCS conference champions in recent years:
2001 -LSU (9-3)
2002 - Florida State (9-4)
2003 - Kansas State (11-3)
Why not agree on a play-off system in which no one gets an automatic bid? You seem to be arguing that a 3-loss team is okay as long as it represents "an isolated down year" for the conference. Either 3-loss conference champions are okay or they're not.
You also seem to be under the mistaken notion that this system is designed to get the best or most deserving teams into the top bowls. It's not. It's designed to bring together the schools that will generate the most interest & therefore the most revenue.