First, I think Bungie needs to drop the focus on competitive PvP. Destiny's PvP isn't fun to play and it will be even less fun to watch. It needs a complete retool, which will take a lot of time. The below suggestions for PvE should be relatively easy to implement.
Weapon trait re-rolling: every weekend when Xur shows up players can spend shards to re-roll one aspect of a weapon. Each weapon has 4 tries until the re-roll option is locked on that weapon. This will allow all weapons to continue to drop with static rolls, but give the player the ability to change ONE aspect of a weapon.
Raid / Prestige Nightfall / Prestige Raid specific weapons and armor that function as a set: a full set of this event specific armor along with 1 event specific weapon will give an armor boost of an additional point in recovery, resilience, mobility to all 4 armor pieces (this would allow the armor to carry 2 traits i.e. Resilience and recovery, mobility and resilience, etc). These events would also have the chance to drop armor modifiers which would allow the player to install one extra mod on one piece of armor.
Raid / Prestige Nightfall / Prestige Raid replay: after the weekly reset, and after players complete these events, rewards will become available again if at least half of the fireteam is comprised of new members. The chance of rewards will drop off by 15% or something like that with each additional play through. However, I believe this will create an atmosphere which will incentivize players to bring clan members into events that aren't usually included. Also, there could be additional reward chances if your fireteam brings in a random player through the guided game mode to carry through the tougher events.
It would also help the PvE experience if the strikes were given hard modes that dropped additional loot / shaders.
If you guys have anything to add, please do so.
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I like your ideas.