The seeding is always going to be totally jacked up for college baseball. It loses tons of money, so they don’t want to make anyone travel…..even the crappiest teams that make the field don’t have to go far. And in an era with conferences that have 16-20 schools, it no longer makes sense to keep 2 teams from the same league from going to the same regional when there are only 16 sites, and 12 or 13 are guaranteed to be in the Southeast pretty much every year.
The prudent thing to do would be ditch the conference tournaments and the autobids from those, unless the conference decides to end its regular season earlier in order to play the conference tourney. Start the tournament 1 week earlier.
8 regionals of 8 teams each are seeded, keep the 16 host sites. Teams are seeded 1-8 for each regional. 1 seeds and 2 seeds host the first round and are paired against each other for the regional final. First round is the same as it is now, except it follows CWS format with days off in between games at each site until only 2 teams are left (hence the 1 week earlier start). No more than 2 teams from the same conference in the same 8 team regional. High seed hosts the regional final round, which remains a best 2 of 3 weekend series. This way there is no ambiguity on who will host if neither 1st round host advances.