Once upon a time, 3B was the deepest position the Padres organization had. Kouzmanoff was the major league 3B, Chase Headley was right behind him (and shifted to LF for a time), behind him was James Darnell, a 2008 2nd round pick; they also had a plucky Vince Belnome and power bat in Edinson Rincon. Kouzmanoff and Belnome eventually got traded, Headley stuck around, but nears free agency and Darnell and Rincon's careers were derailed by injuries.
Once upon a time the Padres had depth at 1B. As recently as 2009 the Padres had Adrian Gonzalez, Mike Baxter, Matt Clark, 2008 1st round pick Allan Dykstra, Cody Decker, and Nate Freiman. That depth has slowly eroded over the years. Baxter is a journeyman who pops up in the majors as a lefty bat now and again. Clark was a solid AAA slugger, but went off to ply his trade in Japan. Dykstra was traded to the Mets. Freiman was taken in the Rule 5 draft by the A's. Cody Decker sticks around, tries out his glove at various positions, doesn't get an younger (he's 27) and never gets love from scouts or the organization. And, of course, Gonzalez we know. He was traded for a 1B, Anthony Rizzo. Who was then made expendable when the Padres acquired current starting 1B Yonder Alonso. A lot of shuffling, but no increase in depth.
What we have left is the aftermath of this bygone era. Darnell and Dykstra should have been in their prime right now. Rincon is still just 23 years old, but the club had to give up on him. It's things like these that have left the upper minors a bit barren along with a draft focus on up-the-middle players (pitchers, catchers, shortstops and second basemen).
Top: Chase Headley
Promising: Yonder Alonso, Kyle Blanks
Grade: C+. Headley's impending free agency and his injury/hitting issues over this season and last make his presence not that impactful when you are looking at depth. Alonso has had his one injury and hitting struggles, but the team has a lot of control over his contract over the next few years. Blanks proved again he can still rake at AAA and sometimes does in the majors, so no one is fully counting him out, but you only get so many chances.
Top: Tommy Medica
Depth: Cody Decker, Alex Castellanos
Grade: C+. Medica got a B- grade from minorleagueball.com so he get to be called a top prospect here. He had his moment in the sun at the end of 2013, but 2014's big league audition made people think he'll need some AAA work (which he skipped over last year). Decker is working hard to make himself useful to the organization any way he can and is a good player to have around just in case you want to throw the kitchen sink at the 1B spot. Castellanos can barely be called a 3B as his defense is not an asset and his bat seems to be in hibernation. Still he can be called depth even though he recently got removed from the 40 man roster.
Grade: F. While the team isn't running out 30+ year olds at 1B and 3B in San Antonio the guys that are playing those positions have very, very little shot of helping in the majors. I almost called Lee Orr and Jason Hagerty depth, but I thought better of it. Sorry guys. Jace Peterson was playing here before his big league call up, but he mainly played SS so he's disqualified for 2 reasons.
Promising: Gabriel Quintana
Depth: Duanel Jones
Grade: C-. I'm being a little generous by calling Quintana promising as many of the prospect gurus (especially at minorleagueball.com) don't back it up. I've see him play and followed his stat lines and he seems to have a bat that will travel. To the majors though? That's something to wait-and-see. Jones was once a more touted prospect, but his bat eluded him last year. He's still just 21, so I won't count him out.
Top: Dustin Peterson
Depth: Jake Bauers
Grade: B+. Peterson is a top prospect that is bordering on elite (minorleagueball.com had him in their top 150 prospects in baseball). He is the only worthwhile 3B prospect in the entire system. Bauers is quite young and intriguing, but needs to have a good season for the TinCaps to be more than that. Franmil Reyes isn't listed but he's an an OF that is already huge (officially 6'5 240) and may end up at 1B. He has the bat for it. Fernando Perez' bat is also good and he has split time between 2B and 1B.
Depth: Carlos Belen
Grade: C+. Belen played as a 17 year old last year mostly with the Padres' DSL team and a little bit for their Arizona Rookie League team. He showed some pop in the DSL. Franchy Cordero will get included with the middle infielders, but there is talk that he could end up at 3B.