I've tested this over the weekend and I've gotten fantastic Minor league stats throughout 25 year stretches, but it does come with a moderately high PITA factor.
Step 1: Go to the link below for the 2012 stats for each Minor League in the game
Link:
2012 Minor League Baseball League Encyclopedia - Baseball-Reference.com
Step Two: Go into the league menu and choose the first Minor league, the International League
Step Three: Go to League Setup>strategy tab where the league totals are located. Input the correct league totals for the league(BABIP will have to be figured out on your own the formula is Hits - Home Runs/At bats-strikeouts-home runs + sac flies)
Step Four: Check the automatically adjust league totals modifiers for accuracy box(that and the box below will now both be checked)
Step Five: Very Important! Click the league menu tab and go to the league home screen, from that screen choose the next league then begin again from step two.
All in all it should take about a half hour to complete but it is absolutely worth it to have accurate minor league stats