That will dwindle the player base drastically. The fact that Bungie can't separate the two is just another example of how bad this studio is.
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The two shouldn't be separated completely. That is one of the things that makes destiny destiny. They should find a way to make perks work differently against guardians or create perks that work really well in pve scenarios that are unlikely to happen in pvp. If you don't want to take the stuff you earn in pve to pvp then go play cod.