MichSt had troughs worse than FCS, but that was in 2004 before they remodeled the stadium. I guess they didn't extend the upgrade to the "facilities."
Colorado has ONE women's restroom to serve the entire west side of the stadium (the side with the 5 story pressbox), and it's in the fieldhouse behind the stadium toward the horseshoe end. At the 2010 BU game, my wife and mom left when halftime started and got back to the seats after BU had run a 7 minute drive to start the 3rd quarter.
Rice has the "step up on a brick ledge and let if fly into the wall," as does Texas St. But Michigan takes the cake on that design. Huge restrooms in the corner of the stadium, with a ramp leading up to the women's and a ramp leading down to the men's. Once you get inside, it's practically the size of a Bucee's restroom, with 6 or 8 rows of 5-foot high brick walls to line up to. Plus the continuing cascading waterfall down said walls drowned out the sound of several hundred all going at once.