Gymnastics - there are regionals for women, not for men. Both genders invite both teams and individuals.
Swimming - no regionals, two qualifiers -- auto standard, and then backfill with B standards (like track used to do). A couple years ago, they made a good decision of removing relays from the qualifier pool. Rather than having those athletes count against the entrant cap, they make the schools pay for them. If a team has 1-3 athletes qualified individually, then they can swim any relay that has an "A" standard, and can bring up to four additional athletes on their own dime. If a school has 4+ athletes individually qualified, then they can swim any relay with an A or a B standard, and can bring up to four additional athletes on their own dime (still subject to an overall roster cap of 18 athletes per team, divers count as .5 people). Conceivably, you can set the world record on a relay and not swim it at NCAAs if non of your athletes qualify individually.
For track, I think you have three possible alternatives to either (a) current or (b) descending order.
- take the cross country model. Run nine regionals, take the top two teams and then like two individual qualifiers per event to nationals.
- take the wrestling model. Establish the number of bids each qualifying conference (6+ teams) receives in an event from a rolling model of previous years, then have 2-3 at-larges per event that are selected by a national committee.
- take the IAAF model. Each conference is a "nation", gets up to three qualifiers plus maybe a fourth for the defending champ per event, pick 'em however you'd like (conference championships, descending order, T&F News Rankings, whatever)