Bad juju needs a buff for it's impact and clip size (right now most rare pulse rifles right now are way better both in pve and pvp) Thorn gets a buff for it's impact and reload speed and around a clip size of 7 bullets so the last bullet upgrade is still useful) VM just restore it to it's former glory and don't listen to the cry babies it's the hardest gun to attain and it should feel special ( no I don't own one and actually got destroyed by it more than once in pvp) and as for Pocket Infinity just increase the clip size to 5, I mean nerfing it from 8 to 3 clip size was to much...
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I think the best solution would be to differ between PVE and PVP. I realize that this would require huge efforts but I think it'd be worth it. I understand everyone who wants the VM to be special in PVE, but it was way too strong in PVP and took away all the fun. So either Bungie finds a good compromise or they need to think about seperate perks and stats on weapons.