Personally I think all of the owners should be cut the fuck out, the federal government should operate the league, the cities run the teams, and all the player salary money goes into a pool and is split up at the end of the year based upon the actual on-field statistical performance according to formula, with a high minimum salary going to everyone.
There's a lot wrong with the way players are paid. The first thing wrong with the system is that owners get anything at all. The second thing wrong with the system is that the players are indentured servants for what is likely to be their most productive years. Most players who are good enough to play at the MLB level aren't even going to reach FA through the arb process normally: they'll hit FA after getting cut first. The third thing wrong is that players who aren't good anymore like Adam Dunn as an excellent example or Chris Davis now, who aren't even MLB level anymore, still keep getting all of this big money from the system that doesn't go to the players who are actually producing.
There's too much to actually fix within the context of MLB. It'll never actually be a fair system for the players and especially it will never be a fair system for the public and the tax payers.