I am not going to say that I came up with this, becuase I did not. However a user on his website, minorleagueball.com, made this post and I thought I would share it over here. Our system obviously doesn't seem so bad, but our 2006 draft looks pretty poor. Anyways, here is what he says
I ranked all 30 systems based on John's letter grades from his book (printed with permission). I also ranked the '06 drafts accordingly. My methodology was as follows: 1 point for every C+, 2 points for every B-, 4 points for every B, 8 points for every B+, 16 points for every A-, and 24 points for every A. As you can see, I weighted top-end talent pretty heavily. But some teams were able to rank very highly without any elite prospects, through a lot of depth. Please feel free to disagree with my methodology, as it does very much favor teams like the Royals, who have more depth than I thought but mostly have the best three prospects on any one team. Anyway, here are the teams with their rankings and scores, separated into easily separated tiers:

1. Tampa Bay Devil Rays 115 (wow)

2. Colorado Rockies 87
3. Arizona Diamondbacks 84
4. Kansas City Royals 82

5. Minnesota Twins 76
6. New York Yankees 73

7. Los Angeles Angels of Anaheim 67
8. Los Angeles Dodgers 66
9. Boston Red Sox 66
10. Cleveland Indians 64
11. Milwaukee Brewers 63

12. Cincinnati Reds 58
13. Houston Astros 58
14. Atlanta Braves 57

15. Florida Marlins 51
16. Detroit Tigers 50
17. New York Mets 50
18. Texas Rangers 48

19. Chicago Cubs 43
20. Toronto Blue Jays 42
21. Baltimore Orioles 42

22. San Francisco Giants 38
23. Oakland Athletics 38
24. Pittsburgh Pirates 36
25. St. Louis Cardinals 36
26. Chicago White Sox 35

27. Washington Nationals 31
28. San Diego Padres 29
29. Seattle Mariners 29
30. Philadelphia Phillies 27

And here are the '06 drafts:

1. Detroit Tigers 21
2. Boston Red Sox 20
3. Los Angeles Dodgers 19
4. San Francisco Giants 18
4. Tampa Bay Devil Rays 18
4. Washington Nationals 18
7. Arizona Diamondbacks 17
8. Kansas City Royals 16
9. Minnesota Twins 15
9. New York Yankees 15
11. Baltimore Orioles 14
12. Saint Louis Cardinals 13
13. San Diego Padres 12
13. Seattle Mariners 12
15. Pittsburgh Pirates 11
16. Cleveland Indians 9
16. Oakland Athletics 9
16. Texas Rangers 9
16. Toronto Blue Jays 9
20. Atlanta Braves 7
20. Houston Astros 7
20. Milwaukee Brewers 7
23. Colorado Rockies 6
23. Philadelphia Phillies 6
25. Los Angeles Angels 5
25. New York Mets 5
28. Chicago Cubs 4
28. Cincinnati Reds 4
30. Chicago White Sox 3