Each league chooses how its NCAA bid will be awarded. If a league wants to give it to the regular season champion, that's totally within their power. Colleges can make it happen. And yet they choose to stick with tournaments to decide the AQ.
The ratio of bids to teams is fixed at 1:6 across all DIII sports. Want more bids, need more teams. But as has been pointed out, that means colleges starting new programs, which typically (not always) means lower-quality teams in the lower-quality leagues. I'd love to see the tournament expand, but that's the downside.
If the objection is AQs overall, keep in mind this is DIII sports. Student-athletes, access and fairness, etc. Part of the point is that the little-guys get a chance at a dream too. Otherwise we might as well be DI football.