A few of us worked on something similar a few years ago. We learned that you cannot achieve truly equitable results if you hold onto "protected rivalries" - it just isn't possible. So you have to create a fluid system that does away with preserving traditional games that don't fit this new era.
I was able to do it pretty well for the BIG, with two protected rivalries per team. I made sure to balance the schedules for the top six teams in the conference, which did end up making the schedules for the bottom of the conference less balanced, but still much better than exists with today's divisions.
In my concept, you make the conference schedule every two years, with a home and home series for each team over the next two years. Then, you reset the schedule for the next two years based on how the teams performed during the previous two seasons, again working to balance the schedules for the top six teams. It's not perfect, but better than the current scheduling methodology.