As far as we know the impact of prestige hasn't changed since the switch to 3.0. I haven't cared much about recruiting since 3.0 came out, but I think it's fair to say that in 2.0 the difference between an A-prestige D3 and a C+-prestige D2 was comfortably south of 25%. I'm estimating very conservatively there to try to keep other coaches on board with the assessment; my best guess is that it's something more like 17-18%. What I really don't know is whether AP are the same amongst divisions. The most likely assumption is that yes, they are, and differ only by the prestige advantage. In which case if, as shoe3 pointed out is entirely possible, they are 400-500 AP ahead of you, it's not unreasonable for you to be behind. If they offered the start/minutes earlier and got more multipliers on the other actions, that helped too.
I suspect that it wouldn't be all that unlikely for an A D3 to actually have a multiplier advantage over a C+ D2 if the preferences favored the D3. I haven't had a difficult time at all battling D2s in 3.0. Of course the one way you can really get burned as the D3 school is if the player has an earlier signing preference and you never really get into play. But if you can stay ahead, you can easily outbattle one division up.