It's fine to prefer one over the other, but id prefer people do so while making actual points. AA had several strengths, but also left the entire system gutted and the roster aged and declining. He pushed the chips in, and ultimately failed. All of AA's credit was building up the system to the point where he could go all in. He was also great at gaming the Comp A and B system when it was still around which one could argue was alrgely responsible for having such a full system. Getting 2-4 extra picks in the top 2-3 rounds never hurts.
I dont even know why people bitch about Shapiro when it comes to team and roster, he has nearly nothing to do with that. Shapiro is probably the best front office guy the Jays could hope to have right now to do what they need doing from a business and Rogers Center building perspective.