Pop is one of the most widely respected coaches in the league, so I doubt he's the problem. His system, however, may be one of the culprits.
1) The Spurs system is notoriously nuanced and complicated. If you had to do a job, would you want to it the simple and fun way, or the difficult and complex way? I think some players just wouldn't want to put in the time, and know they wouldn't stick around long if they didn't. They also know that they will have to give into the "team concept"....meaning they can't try to constantly put themselves in the spotlight. With most NBA players being alpha dogs, and also wanting to showcase their skills to land bigger contracts, that probably doesn't sit well.
2) San Antonio is not a "premiere destination". Sure, its a nice town...but there's no beach, no mountains, no big money market, not a lot of night-life....it's a family town, and not a lot of NBA players are "family guys". Outside of that, about the only thing it really has going is cost of living and no state taxes.
3) Spurs are known for being fiscal, and also don't have a lot of cap space. That means they don't overpay their players, and they make them earn what they do pay. Players are more likely to get a big payday from a team that throws its money around, as opposed to coming to San Antonio where they will be pressured to take less money.
4) Like it or not, the Spurs aren't contenders anymore. They aren't far off, but they are still on the outside looking in. I'm sure players would rather play for a playoff team than a cellar dweller....but they'd also rather play for a true contender than a possible pretender.