Each sport should have its own association to set its rules, sponsor its championships and negotiate its TV rights. Yes, that increases the number of bureaucracies, but none anywhere near the size of the NCAA and the major conferences. Within each sport conferences that make competitive and economic sense can be assigned or formed. A Dallas Baptist or Cal State Fullerton are major players in baseball, Villanova and Gonzaga are basketball elites. Most minor sports need conferences to be regional to cut down travel. Why do we have to be in the same conference in all sports?
At first glance you may say it would be impossible for colleges to organize themselves in every sport apart from an overarching national body like the NCAA or without conferences that oversee all sports. But, that is exactly what club sports do. The revenue sports like football and basketball would need larger organizations because of the money involved. But, each sport would be able to organize itself to maximize efficiency, competition and marketability.