Quick question - as it is currently set up, you cannot offer minor league FA (at the start of the season) any bonus money or anything other than a minor league deal (w/ invite, but that wouldn't apply post-draft) unless you want to give the guy a ML deal. As a result, I often seem to lose on minor league FA because the player likes the lack of depth in another franchise more (he may have better chance of progression, playing time, etc.).
With your "addressing" of the post draft minor league FA rush, would the logic work the same way? Wouldn't you, in effect, be punishing owners who maintain better minor league depth, because the former-11th-round-pick-who-is-a-FA-under-the-new-system will choose the poorly run franchise where he'll be more likely to get 500 PA right off the bat?