Given the limited (or zero) TRUE non-conference play for all schools this year, (Michigan Tech for example has 18 conference games plus 10 additional "non-conference" in-conference games) I think simply giving two invites to all conferences makes the most sense for the NCAA tourney. Let the conferences do what they wish with those bids. My vote would be one for regular season champ, one for post season champ. If both are the same team then the second place regular season team fills the second slot.
AH, Big, ECAC, HE, NCHC, WCHA x 2 = 12 slots
Give one additional tourney slot to conferences with 10+ teams to be awarded as the conference sees fit (regular season runner up, post season runner up, blind draw, whatever)
AH, ECAC, HE, WCHA x 1 = 4 slots
There's your sixteen team field. Sorry ASU and LIU, everyone is making sacrifices this season.
Anything based on media/coaches polls, human committee, etc will be a disaster so just set the rules before the first puck even drops next month so everyone knows the plan going into the season.