Do you really believe the changes in the 2012 CBA "severely messed up" the Rule 4 draft, or is this more "I don't like it?" To me, it was actually a pretty smart compromise. The owners got a guaranteed limit on new entry costs (at an actual lower cost from Day 1) and the players got more money at the MLB level by screwing their non-voting "brethren." Remember the stink Boros made after Appel wouldn't agree to sign for $6.5M in the 2012 draft and went unsigned to the Pirates. The Pirates walked away from their best offer and took the replacement pick in 2013 and Boros swore he would bring the new structure down in the courts because it was unconstitutional, unpatriotic and unAmerican. But here we are.
In 2011 six players received bonuses > $5.0M (top of $8.0M); in 2012 you had 1 >$4.8M (top $6.0M). In the three years leading up to 2012 you had an average of 6 players go unsigned in Rounds 1 to 3: starting 2012 the average was 3.3 in the subsequent three years, and is about one now. The replacement pick completely changed negotiation dynamics. In fact, in 2011 one of the $5.0M bonuses went to Josh Bell in Round 3 -- guarantee you no player will receive a $5.0M bonus in round 3 of the draft again.
I'm not sure how the owners would accomplish this same outcome with just a big pot of money -- think Boros would care about the team's need to make "fair offers" to the rest of the team's draft picks (unless he represented them) if he was negotiating for Pick 1-1? I think the slotting, replacement picks and "sign or lose the slot money" approach has been a boon for the owners, and to an extent the MLB players. This is not unique to MLB. In fact the NFL owners and union basically drew a map for MLB with their NFL CBA the prior year. The impact was as expected (from PFF):
The average yearly salary for a(n NFL) player selected in the first round of the 2013 draft was $2,776,787.70. In 2010, the last year of the old collective bargaining agreement, the average yearly salary for a player selected in the first round was $4,848,126.25.
On the surface, a savings of $2,071,338.55 may not seem like a huge chunk of change, but it is. One has to take into account that the salary cap in the last year of the old collective bargaining agreement was $112.1 million. In 2013, the salary cap was $123 million.
This, in turn, means a first-round pick under the old collective bargaining agreement made up 4.3 percent of a team’s overall cap number. Under the current collective bargaining agreement, a first-round pick makes up 1.6 percent of a team’s overall cap number.
I'm sure the same is true for MLB teams (to a large extent), I'm just not sure where to get the data. But I don't think it severely messed up the draft.