First you need to decide what you want in the tournament. The best teams, or the teams that have done the best. (I’m just talking about the at large teams, I’d never want to do away with the automatic qualifiers).
The NCAA goes both ways on this, sometimes emphasizing recently played games, sometimes considering close losses. I’m firmly in the I want the teams that have done the best, by winning. I don’t care that you’ve got a team that in paper should is better, if you don’t get Wins, it doesn’t matter. Similarly if your star player is hurt, I’m not dropping your seed or kicking you out or putting you in. Can you imagine the NFL eliminating a team’s bye because their QB got hurt?
So using actual winning and not perception as a criteria, a method similar to the Soccer World Cup could be used. Conferences are ranked on past performance and then each conference gets a set number of spots in the tournament. Some leagues get 5, some 6 some 7 some only 1 or 2. Fans shouldn’t have to guess as to whether their team is in the playoffs.
Alternately an RPI like formula could be used, where you get points for beating people, and more points every time they win. But losing is losing. No points for that.