Don't expect a less "idiotic" arrangement if MLB changes things. When you get down to it, all the Rule 4 draft rules - the current ones, the proposed changes, the rules going back to 1965 - are a bit idiotic, if your goal is anything other than just cutting costs. Of course, that's not surprising, given that the draft was implemented to cut costs, and essentially all the changes since 1965 have been targeted at containing costs.
All this, because MLB will not implement serious revenue sharing - which would largely eliminate the financial advantage certain clubs have due to local market size, etc. All this, to keep total costs down to a level that at least most clubs can compete, even with the gross financial disparities - which of course means that the big-market clubs can consistently reap huge windfall gains. (Which is why the big-market clubs have always opposed serious revenue sharing.)
Whatever the changes to the draft rules, the purpose and effect will be contain MLB's costs, with little or no regard to the welfare of the game, nor its "competitiveness," no the impacts on partners (e.g., minor league owners, fans, cities). It will be all about the benjamins.
And inevitably, since some clubs will continue to have huge piles of money they're restricted from using in a lot of ways, those clubs will find other ways to use their financial advantages to get an edge on the field, over other clubs who don't have the dollars to play the same games.