Why does their need to be a "solution"? What is wrong with limiting exotic gear?
The Crucible is not a separate game. It's another part of Destiny. It is meant for your character to seamlessly transition between all parts of the game world.
What you want basically segregates the game world, just so you can wear full exotic sets in PvE. (And for what? So you can feel like a badass going easy mode on the AI?)
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But the Fallen were OP, we need all the help we can get. [spoiler]On a serious note, just keep with the limited amount. We haven't even tried it yet.[/spoiler]