In general, the runner-up in the metro and niagara regions will usually be pretty bad, so it doesn't make sense to guarantee them a spot.
Regions rise and regions fall. When I ran back in the 90s, NY was a region unto itself, and we'd send 3-4 teams to nats every year, and have someone podium most years. The system should be agnostic to that.
I'm just not understanding how people think that Brockport, who ran Geneseo tough twice (SUNYAC and regionals), to then see Geneseo PODIUM and them watch at home, is somehow no biggie, but leaving out a Tufts, Otterbein, etc would be rank injustice.
The committee has biases about which regions are "strong" and which are "weak" that run too deep. Great Lakes got a good run from Calvin as a fifth seed, but they were another outlier, 2/3/4 went like 28th/30th/31st or something like that. New England aside from Williams also tend to be near the bottom, but seem to get 4-5 teams yearly.
Two at large bids per region still gives you 12 at large bids. You could still easily go 4-5 deep in a stronger conference like Midwest if you think they deserve it (because two are already in). Or, have a rule that you can't let a 5 seed in until all regions have a 2 seed in. In the balance of "let them sort it out on the course" and "there needs to be allowances for stronger/weaker regions" the committee is making bad calls and the mistakes are always in favor of the "stronger regions". Let them sort it out on the course.