Sorry but with a 16 team league its the only way to insure that each side plays one another. Go to 2 8 teams divisions, and you are only playing a team in the other division once every 4 to 5 years.
Not really. Can have a single conference or 2 divisions and set up "virtual" pods or protected opponents- whatever you want to call it. Just play the same 3 protected schools each year and then rotate between the other 12 schools based number of conference games each season.