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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The problem is that Bungie won't seperate pvp from pve like most devs do. So you have two classes of players fighting for control of the game's gear and abilities. One who wants them to be powerful and distinctive is their differences..,..pve. The other was them to be bland and the same so that "skill" rules the day....pvp. The two camps have incompatible needs, so they're being pitted against one another.