I think this whole issue divides down into two separate trains of thought, both of which deal with the concept of fairness. Is the national championship meet supposed to include the best possible teams? Or does it want equality across the regions. Under the old structure, with the caps- it made sense that the NCAA was attempting to try and have equality spread across the regions, hence why the south gets 2 auto bids despite in most years deserving 0. The midwest however, always tends to have 8-10 teams rated in the top 35 and if a team had a bad day at regionals. they would find themselves on the outside looking in. However, after the caps were taken off, I thought the purpose was to truly make nationals the "elite" field it was supposed to be in the first place, by allowing regions such as new england and midwest to get more teams who deserve to be there.
This year clearly calls into question the current system. From a completely unbiased viewpoint, both Plattville and Oshkosh should be in the national championship meet. On their good days, both could be top 15, if not top 10 on a great day, whereas teams like Calvin really haven't done anything the entire season to warrant an at-large bid.
Some pundits will say that it doesn't matter because Platville and Oskosh wouldn't win trophies anyways, so who cares? If that is the case, then who cares about the south getting any bids? They aren't going to win trophies either.
At the fundamental level, I believe the NCAA needs to clarify what the national championship meet is for- do they want the best teams there or do they want a regionally diverse field. And if they want the best teams there, they also need to develop a clear cut criteria to selecting teams as well, such as the system laid out by Division 1.