I'm betting the Pac-10 will be the stronger football conference. Here's something I found on the internet from an old USA Today article. It broke down the conferences from 1998-2007. I think it holds some merit considering the SEC has won the NC each year since 2007. From here, you can see where the Pac-10 already ranks second. Now, by taking half of the Big 12 including the two teams that have won a NC in the past decade it makes an even stronger argument that the Pac-16 will be a stronger football conference than the Big 10. The Big 10 actually comes in last considering that Miami is now in the ACC. We could go back 20 years, and things still don't look real good for the Big 10 only picking up one more NC in 1997. I don't really think history going back more than 2 decades has much merit here considering a couple of coaches who notched NC in the last 15 years have already been fired or forced from their position.
National champions by conference
SEC (3) Tennessee (1998), LSU (co-2003), Florida (2006)
Pac-10 (2) Southern California (co-2003, 2004)
Big 12 (2) Oklahoma (2000), Texas (2005)
ACC (1) Florida State (1999)
Big Ten (1) Ohio State (2002)
Big East (1) Miami, Fla. (2001