The NCAA needs to make FCS (and D2 for that matter) more attractive. Right now there is just too much incentive for programs to move up to FBS in order to play the cupcake role in football.
Here's my solution:
The NCAA should require average home attendance of 20,000+ and cummulative attendance of 100,000+ to play at the FBS-level. Then enforce it. This would move all of the MAC, WAC (2012) and SunBelt to FCS. Only Temple, UL-Monroe, and Central Mich would still qualify for FBS, and only narrowly. All other current FBS schools meet the requirement, except Nevada (but they should easiliy by 2012 when they begin play in the MWC).
Appalachian State, Montana, and Jackson State would qualify to move up. Old Dominion would come close. But no one else in FCS would even come close to qualifying based on those attendance requirements (including UMass and NDSU).
Then the NCAA could allow FBS teams to count 2 games against FCS opponents towards bowl-eligibility (which, after the change, would actually make schedules harder rather than easier because of how BCS-conference teams often pad their schedules with multiple games against opponents from these three conferences).
The NCAA should also do something to make D2 more attractive than it currently is.