I'm voting for JPR over AA, though it is a really close thing.
I feel like both have pros and cons like anyone, and both have been royally f***ed by ownership (Wells signing on JPR by Godfrey instead of trading him to LAD for the rumoured Kemp and Bills package) and AA has been f***ed by the compete now instead of continuing a steady rebuild of the organization.
In an ideal world we'd have AA as the GM, running the scouting department for pre-draft and international talent while dealing with the major league team and the media and JPR as an assistant GM looking for players people have given up on (Bautista, Zaun, Encarnacion, etc.) as well as looking through the minors for guys that can contribute at the MLB level, things that he was really good at.