It takes some of those "cream of the crop" kids signed out of HS a few years to catch up. In the meanwhile they are being kept on teams and being given playing time due to their potential more than their current ability to compete. In many cases they aren't as good of players at the moment as college players who will never be drafted.
I think you can look at how pitchers coming out of D1 fare in short season ball and A ball and get a pretty good idea how the minors match up with D1. D1 pitchers usually do pretty well in short season A. Full season A ball is another story and a fair jump upwards. I think a top D1 (let's say top 50) is as good as an average short season team but would get trounced day in and day out by a full season A team, although obviously a good college pitcher having a good day will be able to keep their team in a game. The short season team is still weeding out players and has a mixed talent base while the full season A team has done some of the weeding and is going to be too deep for a college team.
I got into a long "discussion" on this subject once before so this will be my only post on this one.