A couple of questions: What is the purpose of the draft? And does it fulfill this purpose?
If the purpose of the draft is to provide equity in the distribution of talent (the Karl Marx model), the draft fails. Year after year, low market teams take into account signability issues before drafting. Instead of taking the best available player, they often take the best signable player. This creates a problem, but only if you believe in equal access to players. If you believe that teams with more resources should have greater access to players (the Adam Smith baseball model), the draft in its current form is acceptable (in this regard). The draft has other problems, but that will be for another day.
Those that believe in greater equity have called for a strict slotting system. This would do much to solve the above-described problem and it would save owners money. But where would this money go? Would it go to owners' pockets? Would it go to boosting MLB salaries? Or would it simply be hidden in an offshore bank account?
The money saved if such a system were implemented should go to minor leaguers. The minor league player has been left behind while the rest of baseball high dives into Scrooge McDuck's vault. With wages hardly increasing in 35 years, many minor league players are struggling as the rest of the game profits from a popularity boom. If money is to be saved on signing bonuses, measures should be taken to ease the burden on the minor league player, many of whom find themselves in vast amounts of debt.
This, of course, will probably never happen, as nobody is there to fight for the starving minor leaguer. The MLBPA will insist that any money saved must go to MLB salaries, and owners will oblige. Or perhaps another boost will be given to 40 man salaries, as was done when the Rule 5 draft changes were made a few years ago. This helped out a whopping 2% of minor leaguers, and only helped out those already on the cusp of making more money than the President.
These are just my thoughts. But nobody will listen to me, because I'm just a poor minor leaguer. After all, I'm not even a prospect anymore, so who cares?