My way:
What I often do is look at scouting ratings, especially if you have a rather old head scout running the show, e.g. I usually 'stash' a good scout in the Assistant GM slot in order to have one available if my head scout retires.
Then, I would look at their overall roster strategy. If you are trying to rebuild with a strong minor league system, having an assistant GM that prefers veterans and have him handle the minor league system most likely won't be effective I guess
Option Two:
http://www.ootpdevelopments.com/boar...istant-gm.html
But if all of that that really impacts your team alot and how, I don't know. My bet is that the roster strategy will influence things tho.