Keep the current BCS format and use it to determine the Top 4 teams at the end of the regular season/conference championships. Yes, there will be an argument about who gets the 4th spot, but that's a better argument to have than who gets the 2nd spot. There's always an argument about the last spot. Just look at March Madness. However, to maintain the value of the regular season, something very important in college football, you can't expand to 8 or 16 teams. A plus-one system still makes each week just as important as it is now.
In order to follow the lines of historic value and thus keep the bowl system as intact as possible, you keep the current BCS bowls as they are, and let them rotate the semifinal games each year. An actual bowl game no longer determines the national championship, so as far as I'm concerned the NCAA has already compromised the old system enough to manipulate it this much more.
The designated "National Championship Game" is already part of the BCS, but with a plus-one system those teams would not be pre-determined. In theory you are losing ONE pre-determined BCS game, so adding a game like the Cotton Bowl to the BCS structure wouldn't hurt, although for explanation's sake I'll leave it out for now.
Here is what a good plus-one system would look like (at-large substitutions would be applied for Bowl tie-in teams who finished in the Top 4):
2010
Rose Bowl - Pac 10 vs. Big Ten
Fiesta Bowl - Big XII vs. At-large
Sugar Bowl - BCS #1 vs. BCS #4
Orange Bowl - BCS #2 vs. BCS #3
National Championship Game in Pasadena, CA - Sugar Bowl winner vs. Orange Bowl winner
2011
Rose Bowl - BCS #2 vs. BCS #3
Fiesta Bowl - Big XII vs. At-large
Sugar Bowl - SEC vs. At-large
Orange Bowl - BCS #1 vs. BCS #4
National Championship Game in Glendale, AZ - Orange Bowl winner vs. Rose Bowl winner
2012
Rose Bowl - BCS #1 vs. BCS #4
Fiesta Bowl - BCS #2 vs. BCS #3
Sugar Bowl - SEC vs. At-large
Orange Bowl - ACC vs. Big East
National Championship Game in New Orleans, LA - Rose Bowl winner vs. Fiesta Bowl winner
2013
Rose Bowl - Pac 10 vs. Big Ten
Fiesta Bowl - BCS #1 vs. BCS #4
Sugar Bowl - BCS #2 vs. BCS #3
Orange Bowl - ACC vs. Big East
National Championship Game in Miami, FL - Fiesta Bowl winner vs. Sugar Bowl winner
If the NCAA wanted to take maintaining historical value a step further, they could determine the semifinal sites each year based on the Top 2 teams and their respective BCS Bowl tie-ins (i.e. if the SEC Champ was in the Top 2, their game would be at the Sugar Bowl) but I have a feeling the Orange Bowl wouldn't appreciate that. I doubt we'll see something like this anytime soon, but as you can see, it's really not that complicated. It stays as true as possible to the current system and ideals that promote the value of the regular season. It gives even more significance to the current BCS Bowls, since each year two of them determine who plays for the national title. In the current format, none of the four BCS bowls have anything to do with who is crowned the national champion.
I've yet to think of a logical reason why this system wouldn't work.