The single biggest and best thing they can do is what reinsel said, and what others have been preaching for the last few seasons: Make players in the 25-100 range at their position better. Until that happens, the talent discrepancy between the haves and have nots is so big, not much else matters.
Not to mention that this is the most simple, fair way to do it. Having guys skip college entirely after you've recruited them and some of the other suggestions vary from way, way extreme to simply doing more harm than good.
Of course there are other things that can help (improvements to how prestige is determined, etc.). But we had the dodgy prestige system before the most recent change, and mid-majors thrived regardless -- non-BCS teams were exponentially more successful in HD than in real life (and I think that was fantastic for the game, and perhaps the major key to making DI attractive and healthy). But clearly the system for prestige determination in and of itself was not the problem.