So, I don't particularly believe that golden gun is very overpowered in pvp, in fact I think it might be the most balanced of the supers (the solar warlock one might need a buff to movement speed I dunno, but that's another story), but I do think it sucks in pve unless you wanna take out thrall or other low tier enemies.
Anyway, the change I propose would mean a slight nerf in pvp, depending upon how you look at it and a buff in pve. So what if golden gun required a charge and the charge time is proportional to damage inflicted. So there would be a "sweet spot" in crucible, I'd make it fairly short only half a second or so, to kill a guardian, with peak damage being reached after a few seconds. I dont think the gun should auto fire once fully charged like a fusion rifle, but rather hold it like a plasma pistol. Since the golden gun timer itself is your hurry up. This would mean a full charge could deal respectable damage on pve enemies also.
I just pulled these figures out of my ass here, but I think the overall idea isn't a bad one and would address most complaints about golden gun that people have.
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I am using a Hunter and I can say that the Golden Gun in PvP is overpowered. Use cobustion and the Symbiote, you get four shots per Golden Gun use. Each kill makes enemies explode and tht explosion can kill additional people in Crucible. You can kill three people with one shot. A simple bonus to damage in PvE would suffice. Bungie needs to separate the "improvements" they do between those in PvE and those in PvP, which I guess is extremely hard for them.