The problem with the current system is that the regions aren't balanced in any way, shape, or form, and the entire championship field can spin on the whims of one coach. Look at the women's qualifying last year - because Texas sucked all year long, then ran in a shit regional and got second, then it changed the final eight at-large spots from the teams that ran at Wisco to the teams that ran at Pre-Nats. Literally if Texas had placed third, a third of the NCAA field would have been different.
The likely effect of adopting this proposal is that you'll strengthen a lot of the smaller meets across the country. This is what happened with men's golf -- they used to not include team performance in the process, simply the scoring average. A few years ago, they implemented a rule that you had to be at least .500 to be considered for an at-large bid -- all of a sudden, you have teams from power-5 leagues showing up in random tournaments all over the place, not just the same 20 tournaments each year to play each other. They can't take the risk of only playing other top teams, because then you could end up sub-500 and ineligible. So, you have a lot more competitive events happening all over the place, all throughout the year.
Another plus in favor of this proposal is that it nearly doubles the number of teams that earn Director's Cup points, which REALLY helps coaches in terms of showing value to the Athletic Directors (and therefore helps stave off cutting teams). Right now, everyone who places top-5 in their region earns points for the Directors Cup (for those confused: this gives points for NCAA participation to each team, which then creates a department-wide ranking on NACDA.com). That's 45 teams per gender -- places 1-31 go to teams in order at nationals, and then everyone else who didn't get invited shares the points of places 32-45. This proposal would give 72 teams per gender points - again, 1-32 would be reserved for finals, but then the two teams that place 17th in the semifinal races would share points for 33 & 34, 18th sharing 35 & 36, etc., on down the list until teams 65-72 all get five points apiece. That means more teams contributing to the department goals, more happy ADs, more funding (or at least, fewer funding cuts), and a deeper, healthier sport.