I think I would take #1 narrowly over #3. To me, being able to put .900 OPS in the shortstop position gives you a massive advantage over almost every other team. His projections aren't atrocious for SS, so I think you can get away with it. However, if his development gets stunted for any reason (you are unable to sign a quality fielding instructor each of the next 3 years, or if he gets any significant injury), and he winds up at like 80/75/75/83... then you wind up with a 2B who will hit in the .900 OPS range. Still valuable, but not as valuable as the stud pitcher.
So because of that, I would take #1. Even if he misses some of his projections, he's still incredibly valuable. In a perfect world, I like #3 better, but #1 is the safer choice to me. The only difference would be maybe a 40-point difference in makeup between the other. If #3 had 80+ makeup and #1 had less than 50, I would probably go with #3.