ESPN's Keith Law ranked baseball's best farm systems. He's got the Padres ranked 6th just like SBNation's John Sickels. I had the Padres at 6 too. So now we can say definitively that all the experts agree. We also agree that the Cardinals have the best system, but that's about all we can agree on.
My top system from last year graduated several players to the majors, saw a few significant injuries to top pitching prospects but then added a ton of high school pitching talent through a very strong draft. The system's weakness is in near-ready talent, where only infielder Jedd Gyorko and right-hander Casey Kelly are likely to be significant contributors this year, with lefty Robbie Erlin a possible option for the back of the rotation.
So now we just wait for these pimple faced boys to grow into acne scarred men. The ol' waiting game. It's only a matter of time now until the Padres finish 6th in the World Series. Patience will be the key.