This entire thread begs the question: what are we trying to accomplish in our sport? Most coaches who know what they are doing prefer a qualifying format in which their team only has to perform well one time prior to nationals in order to qualify. However, from a spectator standpoint, it makes more sense to have a system that favors consistent performances, like basketball has. If we ever want our sport to attract the fan base that basketball has, we would have to develop a different system. However, I don't think that realistically ever going to happen.
As it is right now, the system allows teams to qualify either by A. earning points earlier in the season, or by B. simply running well enough at their regional meet to make an auto spot. I understand that teams that are in tough regions really can't qualify using B, but everyone knows ahead of time if they are in a region with 2 really top teams, in which case they will need to earn points during the season in order to get an at-large slot. So the current system is pretty good. The only way that would be much more fair would be to bring everyone to one site for a national meet before the real national meet in order to determine the qualifiers for the real national meet, which would be ridiculous.
The only thing that I would say is that I do believe there should be more individual qualifiers. Many cross-country runners do not choose their university based on the cross-country program, but based on their academic interests. These student/athletes should have some kind of reasonable chance to qualify for the national meet, even if they aren't one of the top 50 runners in the country.