Awarding a bid to each eligible conference is the best way to do things. The conference choice of having their tournament champion get the AQ is fine by me as well.
In determining who the best teams in the country are, across conferences, D3 hockey is ill-equipped. Sometimes all we have to compare conferences is 5 or 6 games that feature a team from conference X and conference Y out of hundreds played by each conference. 75% of games a NESCAC team plays are in conference, I'm not sure how many in other conferences off the top of my head but I imagine its comparable. We are always talking about sample size, how can you possibly compare the NESCAC (I'm using them as an example because it's what I know, not saying they are getting the short end of the stick) to the ECAC W based off of a sample size of what, 4 games? For the same reason I think SOS is one of the more overrated metrics out there, an 8-1 loss by Conn College, the 8th place team in the NESCAC, to Hobart, a team tied for the first place in the ECAC W skews the SOS for the entire conference. Do we really learn anything about the comparison of the ECAC W to the NESCAC from that, especially since margin of victory is not considered in any metric? In the same line, Bowdoin beats two of the lesser teams in the ECAC E. We don't learn much about either conference by those either yet those games go a long ways in the SOS metric for each conference. Some of this is may be exaggerated a bit but the point still stands, until there is enough crossover between conferences (and it sounds like we are headed in the opposite direction) each conference needs to be awareded a bid, ECAC W included.