Seed conferences based off of conference dual meet results. If schools face each other outside of the official conference meet, it gets used too (thinking Bedlam here).
Ignore the name of the wrestler entirely. Input the school name during the seeding process.
It's a start and it will ensure that schools are a bit more honest, hopefully.
Edit #1: Not sure how we implement this to NCAAs, but one method to determine AQ is perhaps use the previous seasons NCAA results. Top 24 earn AQ for the conference, with each conference earning at a minimum one (1) AQ - on the chance a conference has no Top 24 placers. The balance becomes wild card (up to nine of them).
Edit #2: Keep NCAA seeding and WC selection the same, as-is. I like it. Match count requirements, RPI, record, etc.
Edit #3: I would also like to see D2, D3, and NAIA each get their champion (or highest accepting placer) a chance at D1 as well. The caveat is that those three cannot participate in the pig tails, so at the very minimum they must be seeded 26-28 at the lowest. Oh! Also conference champions cannot be seeded in the pig tails either!