You can make any team into a PIT/NT contender in a bad conference very quickly. Maybe some people like it, but I think it gets very boring very fast beating up on sims with no competition and no one to chat with on the coaches corner...plus you're always one loss in the CT away from a totally wasted season. So, to me, building a team in an empty dead conference feels like a waste. Point being--I'd pick the most active conference you can find--people to talk to and learn from, some better conference games, and the possibility of getting multiple teams in the PIT/NT and more recruiting money. Quick look at those teams, it looks like Southland/Lamar might be the most active.
There are other factors you could look at as well, the number of available scholarships right away, any holdover sim underclassmen who are decent, etc., but for me the conference is the most important thing. It does depend on what you want to get out of the game and the team.