I'm starting to think that discipline is the only thing that affects (or "effects" as the morons who worked on the game would say) academic prestige. I've been recruiting only players with A- or better awareness and good or excellent discipline ratings, with one or two averages if they're incredible athletes in positions of need. I've been punishing the problem players more than the CPU suggests to get the interest bar down to nearly nothing, but after my 4th season, in which I had a few discipline problems, I lost another star on my academic rating. This was immediately after I entered the offseason, so it was obviously for things that happened during the season, and I don't think it was the number of players leaving early because I convinced something like 6 of the 8 who wanted to leave early to come back for next season. I had 16 seniors "graduate" and only two players leave early (one for the draft, another was a transfer).
So what we have here is a poorly conceived and implemented feature (academic prestige) that is based on another poorly conceived and implemented feature (player discipline). Good job, guys!