Short answer - fatigue seems to be the way to go. the danger of target minutes is a player may stay in the game when tired, and there seems to be a big drop off in performance when players are tired.
some additional thoughts:
I have run press and m2m defenses most of my time in HD.
I have found that I can use target minutes in m2m or zone without much trouble when I have promised starts to freshmen. This allows me to honor the start but not have them getting as much time on the court as they would under fatigue settings and allows the player I want to get more minutes.
I usually take the exhibition games as a practice run to put the guys I like (the better players) as starters under normal tempo to get an idea of how many minutes they can play under the fatigue settings. Then when the regular season starts I have an idea of realistic target minutes that should enable them to not get fatigued.
Anyhow, I prefer fatigue settings and always go that direction in the NT and CT, especially since you don't have to worry about promised starts at that point anyway.