One of the things Padres fans have had to get used to the last few years is hearing that young players the franchise has drafted and acquired via trade are actually quite good. This is quite the turn of events since the blundering of the 1999 draft, the 2004 draft and a farm system that once had Paul McAnulty as its top prospect. That being said, a few different sites have considered the Padres system to have taken a step back this year, but John Sickels still ranks them high and has this to say:
6) San Diego Padres (2): This system is still persistently underrated. Jedd Gyorko is poster boy for that. Strengths: tons and tons of depth, large number of prospects in the B/B-/C+ range, could look even better if recent high school pitching drafts take off in '13. Weaknesses: hitting is weaker than pitching but it isn't bad, especially if Austin Hedges continues to hit. Expensive investments in high school tools players have not panned out (Donavan Tate, Everett Williams).
The number in parenthesis is lasted year's ranking. The full list is found here on Minorleagueball.com. Sickels doesn't mention the injuries that happened to a few of the prospects, which affects the rankings. Casey Kelly and Robbie Erlin are already healthy, but Joe Wieland will be out for a while. In addition, Yasmani Grandal and Yonder Alonso are no longer prospect according to these definitions due to losing their rookie status. Those are probably the main reasons that after ranking number 2, the org is down to number 6. Why would it fall farther in others' eyes? The lack of high ceiling talent that people see as elite prospects. Depth isn't sexy. In Sickels' rankings for Padres prospects he writes:
Fried, Weickel, and Eflin are all excellent high school products from the 2012 draft, if somewhat difficult to grade and rank due to lack of pro experience at this point. I've opted for cautious grades in accord with my general policy, but if they perform well all could be B+ (or better) a year from now.
If I were to guess, Sickels probably sees these three having the potential to be B+ or better (elite prospects) as somewhat filling in the gap of missing elite talent.
Mostly, the whole ranking business is a convoluted process, but overall you can summarize Sickels' assessment of the system: plenty of depth with potential for growth into elite talent. Others might just settle for saying it has a lot of depth.