I've long thought the solution to the non-BCS conference teams complaints about BCS bowl bids was pretty simple: adopt the European soccer style system of promotion and relegation.
For those that don't know, the promotion/relegation system takes the bottom team in the top conference and replaces them with the top team from the bottom conference (in soccer, it's 3 teams at a time out of a league of 20).
I spent a lot of time trying to figure out the best way to do this with NCAA 12, and here's the system I came up with. I'll be using it for one of my offline dynasties and probably doing an online dynasty using this system as well.
First thing's first. In NCAA 12, there are 11 division 1 conferences. You can't delete conferences and you can't add new conferences. So there's an oddman out. I created 5 top conferences (BCS Conferences) and each has a Feeder Conference tied to it.
EDIT (July 22): All right, danknerd went through the trouble of creating all the Ivy League schools in Team Builder (which, if you read through the posts, you'll see the discussion about them, etc), so here's the finalized starting conference set up I'll be using.
BCS Conference: Pac-12
Arizona
Arizona State
Cal
Colorado
Oregon
Oregon State
Stanford
UCLA
USC
Utah
Washington
Washington State
Their feeder conference: WAC
BYU
Boise State
Fresno State
Hawai'i
Idaho
Nevada
San Diego State
San Jose State
UNLV
Utah State
BCS Conference: Big 12
Baylor
Houston
Iowa State
Kansas
Kansas State
Missouri
Oklahoma
Oklahoma State
TCU
Texas
Texas A&M
Texas Tech
Their feeder conference: MWC
Air Force
Colorado State
New Mexico
New Mexico State
North Texas
Rice
SMU
Tulsa
Utep
Wyoming
BCS Conference: Big Ten
Illinois
Indiana
Iowa
Michigan
Michigan State
Minnesota
Nebraska
Notre Dame
Northwestern
Ohio State
Purdue
Wisconsin
Their feeder conference: MAC
Bowling Green
Central Michigan
Cincinnati
Eastern Michigan
Kent State
Louisville
Miami (Ohio)
Ohio
Toledo
Western Michigan
BCS Conference: SEC
Alabama
Arkansas
Auburn
Florida
Georgia
LSU
Kentucky
Mississippi State
Ole Miss
South Carolina
Tennessee
Vanderbilt
Their feeder conference: C-USA
Arkansas State
Louisiana Tech
Memphis
Southern Miss
Troy
UAB
UCF
UL Lafeyette
UL Monroe
USF
BCS Conference: ACC
Boston College
Clemson
Florida State
Georgia Tech
Maryland
Miami (Fla.)
North Carolina
North Carolina State
Penn State
Virginia
Virginia Tech
Wake Forest
Their feeder conference: Sun Belt
Buffalo
Connecticut
Duke
ECU
Marshall
Pittsburgh
Rutgers
Syracuse
Temple
West Virginia
The Ivy League in the Big East league slot.
The leftovers: Independents
Army
Navy
danknerd also made a spreadsheet for the conferences (including divisions, and came up with some nice names for the divisions even) and it's available
here.
I'll be promoting/relegating one team per alignment (five teams total) per season.
There will be one more edit in this post regarding suggestions for what Ivy League teams to put in place of what TeamBuilder teams. The only reason that edit will come is for how rivalries work with Team Builder teams. For example, I'm going to suggest Harvard & Yale replace FIU/FAU in order to keep one of the most important football rivalries in the nation intact.
There are other Ivy League rivalries, but Harvard/Yale is the only actual Football rival within the Ivy League I know of. [EDIT: Untrue. Just found out Cornell/Penn have a football rivalry.]
Other Ivy League rivalries I know of include:
Cornell/Harvard: men's hockey
Cornell/Princeton: men's lacrosse
Princeton/Penn: men's basketball
As for the teams being replaced... I think WKU/MTSU may have a rivalry that can be used, and surely between Akron/NIU/Ball State, there's a rivalry in here, right?
Other rivalries worth noting:
Princeton/Navy
Yale/Army
So, if you play as Princeton, Yale, Navy, or Army in this setup, you should be sure you're scheduling that non-conference rivalry. The game won't count it as a rivalry, but for realism sake...
[EDIT: Version 3 will be incoming. Need to close the gap between Big Ten & MAC.]