Honestly, I think that PvE is getting pushed around because of PvP. All the changes are affecting PvE in a way.
It's not completely bungies fault though, they listened to the community.
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I wish Bungie had approached the game the way Bioware approached Mass Effect 3, where the multiplayer is involved with the story, yet is completely separate from the campaign. I think the best thing to do with Destiny at this point is to have each character have a "Crucible loadout" where everyone has access the exact same guns with the exact same perks, everyone gets one of each type of gun to choose from (ie high rate of fire, high impact, etc). Keep PvE weapons using the same system we have now, they just can't be used in Crucible. This way Crucible would be entirely skill based without god rolls dominating the playing field at all times and PvE won't get shit upon due to god rolls in Crucible.