The current regional weekend is the greatest weekend in the sport and it could remain so even with the expected changes.
The system should include AQ from conference champions like all sports. Yes there will be some crappy teams that get to the regional but so what, they already do. It also should include an at large process that gets the total teams to at least 64 (maybe more). If you can't make the top 64 teams then you really have no right thinking about being part of a championship system. The key is to figure out the process for selecting at large teams. It might be worth checking what they do at NCAA D3. There is less inter region competition. They use some system to extrapolate to fill the field at NCAA championship. It is first based off regional finish and you are cannot advance to NCAA championship ahead of any team that beat you head to head at your regional. This method might work using it at the conference championship level so that if you finished 2nd the third place team cannot bump you out.
The new system should include an avenue for individuals as well. The sport needs to know who the best XC runner(s) in the country is (are). Top (3-5) individuals from conference meet whose team doesn't advance should move on as individuals. The regional should generate top 25-32 individuals from teams that don't advance to championship (32 teams).
Whether the change is a good or bad thing is always going to be debatable. The current system also generates issues. You aren't going to please everyone but I would argue that those who are stuck in the current system need to be ready for change that satisfies the NCAA. There is no reason every single team in the sport should qualify for regionals. It doesn't happen in any other sport.
The "championship season" should include conference/regional/nationals and each of these should influence next potential round (conf to regions, regions to nationals)and ultimately the team champion and All-American individuals.
I have coached collegiately for 30 years and don't want to get stuck just repeating the old way of doing things. I would rather shape and influence how this will work under a new system. The new system should ensure that we ultimately get to a championship of 32 teams plus 32 individuals. As long as we have a pretty good system to select at large and perhaps seeding teams then a new system will be just fine. With 32 AQ's from conference meets you would expect that about10-20 of them would likely be in the top 64 best teams in the nation. In the end your chances would be better as an at large team than they currently are. You would go from trying to select #17-31 teams to selecting #33-64. This doubles the at large pool at a minimum.