Several posters have emphasized that the most important thing to strive for in structuring the NCAA women's hockey tournament should be the experience of the players themselves.
You may be interested in the very different national championship experience of women in another collegiate niche sport, squash, although that experience is not translatable to hockey because of the vastly different geographical profiles of the two sports.
Collegiate squash is not dissimilar to Division I hockey in size. There are 42 women's squash teams altogether, with 15 or so players per team.
Crucially, all teams except Stanford and Berkeley are located in the Northeast, within a bus ride of several good tournament sites which rotate year by year.
Therefore, all 42 teams participate in the national championship each year.
There are five flights of eight teams, top flight (#1 through #8) to bottom flight (#33 through #42), seeded on the basis of a coaches' poll from #1 to #42. Division I and Division III schools compete together, and one or two Division III schools (notably Trinity) make the top flight each year, on merit, not on the basis of autobids. Conversely, such Division I and IA schools as UNC and Georgetown find themselves in the bottom flights.
Each flight of eight teams starts with one round of elimination matches, based entirely on bracket integrity, followed by two more rounds of elimination and/or consolation matches, resulting in a final #1 through #8 ranking which may or may not resemble the original #1 through #8 seeding. All teams are guaranteed three matches.
There are no gate revenues, because admission is free, and no television revenues. The tournament is sponsored by something called the Collegiate Squash Association, whose financing is shrouded in mystery (there may be an endowment), not by the NCAA.
At the end of the tournament all 42 teams gather for a banquet with parents and siblings. High school teammates reconnect.
So the geographic proximity of the participating schools allows for an experience that is both highly competitive and yet completely inclusive and great fun...despite the apparent lack of revenue.
It's a shame that the NCAA won't currently allow women's hockey some of these aspects that actually could translate to hockey's different situation, such as strict bracket integrity and having the participating teams gathered in a single location.
If anybody is familiar with another niche sport, intercollegiate rowing, it would be interesting for us to find out how the Intercollegiate Rowing Association structures the national championship regatta. Rowing is like hockey geographically inasmuch as universities such as Washington and Wisconsin have been among the top powerhouse crews over the decades. I'm under the impression that they gather in the same place and adhere to bracket integrity.