As It's About the Money put it: "they’ve created a league where the 12th pick in the draft is more valuable than one of the game’s better centerfielders, and in which the New York flippin’ Yankees are going to extraordinary lengths to comply with the luxury tax cap."
In the good old days, teams were allowed to spend their resources however they saw fit. If a team like the Mets decided that Michael Bourn, a legitimate MLB centerfielder would make their roster, which did not currently have any, better they could sign him. Sure, they would sacrifice a draft pick, but they could spend extra on talent in other areas of the draft to try to acquire first round type talents who had slipped. The problem is that the best way to build a winning team is through the draft. First round picks, which used to have value, because hey, you could draft potentially good players, now have extra value because they are a license to spend the most efficient money a baseball team can - on amateur talent.
The answer: less regulation. Blow up the hard draft slots. Keep free agent compensation as is, for all I care. But please, MLB and MLBPA, get rid of the absurd hard slotting for amateur talent. Pay the talented people.