Yeah, MLB incentives are different from the NFL or NBA where actual salary structures can be determined by such things (and many other things). But those are leagues with caps and floors (I mean, fundamentally, all NFL teams have the same payroll, and the gap between the richest and poorest in the NBA is also small, even with all the exceptions and luxury tax payers). Apparently this proposal does include something similar (replacing Super 2 with "Elite 2").
Reading more about the proposal - which was purely made using FWAR as an example - it actually doesn't seem that crazy. It would likely redistribute wealth among the players in a way that that wouldn't be popular for all of them though. And the big hole is still how little players get paid in their first three seasons with only limited ways to bump that. If you're going to go to a WAR-based system than a rookie like Ryan Howard should be eligible for that immediately.
Here's how it would work, per sources: Players with less than six years of service would be paid based on a formula agreed upon by both sides. For purposes of the presentation, the league chose wins above replacement as calculated by FanGraphs. A player with more than three years would multiply his career fWAR by $580,000, and the resulting number would be his salary that season. The multiplier for a second-time eligible player would be $770,000, and a third-time player would receive $910,000 for each fWAR gathered in all his big league time. There would be slight adjustments to salaries based on how the player fared in the previous season, but generally the system would pay players based on the fWAR formula.
Beyond that, the minimum salaries would jump to $600,000 for first-year players, $700,000 in their second seasons and $825,000 for their third. Gone would be Super 2 players -- those with the most service time in any given class who receive an extra year in the arbitration system -- replaced with an "Elite 2" plan, in which players who earned All-MLB honors would get a third-year salary bump from $825,000 to $2.5 million.