I don't have the solution fleshed out, but I know the pain ;)

I feel like the GMs should have some control over their minor league stadiums in the system.  I'm not recommending we all get to pick exactly what the park factors are.  My initial thoughts would be to offer us to change each levels park to one of the minor league parks at the same level out of use.  So assuming WIS has roughly 50 AAA parks- you can change with any AAA park someone else isn't using at the start of each season.

For those who preach realism- MLB organizations can choose the location of their minor league affiliates.  More factors than the park itself are involved (location, travel costs, minor league quality, city size/support, attendance, quality of facilities, etc...), but on the whole, MLB teams can select a minor league team that fits their needs once their current deal for the level expires.

The challenge would be to find a system that is simple, fair, and can be ignored if someone wants to.

I think the best solution is no more than a 1 variance from the BL park.    1,1,0,0,0 could only be 0-2 for 1B, 2B and 1-(-1) for 3B, HRLF, HRRF.    Although minor league stats should largely be ignored, you're still drafting your "type"(assuming you have one) of player for your BL park.