John Sickels has the Cubs minor league system rated #10 in his latest rankings. Last year they were 20th. The Cardinals are #1, the Pirates are #5, the Reds are #15 and the Brewers are #23.
10) Chicago Cubs (20): Another system that has improved quickly. Strengths: hitting at the top: Javier Baez, Albert Almora, Jorge Soler, Dan Vogelbach is a very impressive quartet and there is depth beyond them. Good developments with recent Latin American prospects at the lower levels. Weaknesses: pitching is much, much weaker than the hitting. Improving that has to be a priority.
The full rankings can be found over at SB Nation.
That's a pretty nice leap considering one of the biggest prizes of the system last year (Rizzo) is now on the major league roster.