I would like to see Auto-fire become a "ranked" quality, requiring a specific amount of Advantage to activate, similar to the way different weapons have different Critical Ratings. Different weapons have different fire rates, after all. I think this would kill several birds with one stone.
First and foremost, I thoroughly disagree with the +1 Difficulty die for attempting auto-fire. I agree that it shouldn't be easy to score multiple hits, but this is not the way. It makes no sense that I am less likely to hit even once if I fire multiple shots. The first bullet out of a gun is never affected by the fire mode selection. Only subsequent bullets can be affected by recoil at all. If the target is in my sights, pulling the trigger will result in at least one hit regardless of how many additional shots the gun fires. This is even ignoring the fact that the average real-world gun capable of auto-fire doesn't begin to experience any significant recoil until after several bullets have already exited the barrel. Increasing the amount of Advantage required to score an extra hit would go a long way in controlling the uberness of Auto-fire, so the +1 Difficulty nerf would no longer be required for balance purposes.
The binary nature of fire rates has also put a damper on the variety of weapons the book offers. The way the weapons table currently works is that only the Big Guns™ have Auto-fire at all. There is no equivalent of a SMG in the book. There is no equivalent of a bolt-action sniper rifle either, since the closest thing (Heavy Blaster Rifle) has Auto-fire and is vastly more effective when auto-firing than when trying to score a single good hit. It plays more like an assault rifle in this regard. I initially planned to play an Assassin, but when I saw the weapons I said "screw this" and went with Gadgeteer instead. Varying the Auto-fire thresholds would allow for a lot more variety in the weapons.