with 30 teams, shouldn't an average system have 3 in the top 100?
Not really. Here's the breakdown from the 2015 list:
By Organization
7 Red Sox, Mets
6 Diamondbacks, Cubs, Nationals
5 Rockies, Twins, Pirates, Rangers
4 Royals, Dodgers, Blue Jays,
3 Reds, White Sox, Phillies, Cardinals, Padres, Rays
2 Orioles, Astros, Angels, Marlins, Brewers, Yankees, Mariners
1 Braves, Indians, Athletics, Giants
0 Tigers