Pop knows how to utilize talent, Jackson knows how to use stars.
I'm not sure if Pop would have ever won as many rings as Phil even if they switched places throughout their careers. Pop is determined to do things his way without giving a damn about what the players think, not to mention his hate for big egos. So would Pop deal with the y Jordan/Kobe, the locker-room hate between Shaq/Kobe, the trio of MJ/Pippen/Rodman? Well, the first thing he did as GM was trade Rodman... So there's that.
Phil knows how to work with stars, how to earn their respect on the floor while not getting involved in their personal decisions. Pop isn't that kind of player, he's "My way or the highway." I can't imagine Kobe/Shaq/MJ/Rodman/Pippen playing along to that.
With that said, Phil Jackson would shoot himself if he found out his best player was a 38yr old Tim Duncan.