Here's why I would still hesitate to dispense with the automatic qualification. I think it would effectively preclude any mid-major team from ever making the tournament again, unless they already have built up a national reputation (in other words, UConn). You start with the perception that those conferences are weak, so there is very little attention given to them from the beginning of the season. We'd like to believe the committee would not be influenced by that, but the reality is there are only so many hours in the day to watch all of the games which have been played. So when we reach the time to set the tournament field, mid-major teams would not be seriously considered (often-times, rightfully so, but I think a few deserving teams get left by the wayside without receiving due consideration).
This then turns into a feedback loop. Mid-major teams have almost no shot at being in the tournament, so talented players will go elsewhere (or start there and transfer at the first opportunity) so they have a realistic chance of making the tourney. Which effectively means that those mid-major teams are doomed to stay weak, and the level of competition becomes even more stratified than it already is. Once the tournament starts, then you don't have the wide disparity so readily apparent, but it certainly exists.
I think there's an obvious counter-argument to everything I'm saying: the system is already heavily slanted in favor of the rich getting richer. Look no further than who the relaxed transfer rules benefit. Yeah, I get it, this problem is not going to be solved soon. My thinking though, is that I would want the mid-majors to at least have a fighting chance. Without that, I don't see how a small program ever becomes relevant again, and I do not see that eventuality as good for the sport.
Truthfully, I'm not sure how I would solve it. All I can say is I would want some mechanism to for mid-major teams to have a meaningful chance to play in the tournament. If the AQ method is doing more harm than good, then eliminate it, but do replace it with something.