They had this exact discussion on the Dan Patrick show yesterday.
IMO, Gramercy hit the nail on the head. If it were a draft, and I were taking a PG #1, I'd select Zeke just for his ability to score, take over games, and lead by his will.
If I had a bunch of studs already in place and a prime finisher at the rim, I'd take Stockton in a heartbeat because he is more of a facilitator and makes everyone better.
Taking it back to the Dan Patrick show, they were debating the pros/cons of Rondo versus Deron Williams. I actually put Rondo in the same category as Stockton, Williams in the same category as Isaiah from a "skill" standpoint. Watching Rondo play is like watching any of the great team facilitators over the years. He puts it in the right guys hands at the right time, every time. If he needs to, he'll score. He just doesn't make too many bad plays, and a lot of his assists come from the perimeter.
Williams is clearly a better pure scoring threat. A lot of his assists come with him in the paint after his drive has been cut off, which doesn't happen often.
I see the Isaiah/Stockton debate as being very similar to the Rondo/Williams debate. As Gramercy said, it would depend on the other 4 guys on the floor.