The reason is simple. If they left in the ability to trade materials for marks, people would use it as a way to convert vanguard marks to crucible marks or vice versa.
Think about it? You trade a bunch of vanguard marks for materials, then trade those materials back for crucible marks. It eliminates the need to play their god awful crucible mode. It also lets people play exactly how they want to play, so of course bungie can't allow that...
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You could trade for crucible or van marks before anyway....solution is to allow faction purchases with vangard marks. probably something that will be addressed when new factions come out in a week.
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It's still doubtful they'll ever let you get faction gear with vanguard marks. For whatever reason, bungie is obsessed with getting people to play the crucible. If they allowed people to get faction gear with vanguard marks, it's one less incentive to ever enter the crucible. TL;DR Since it's a lot easier to hold rewards hostage than it is to retool the crucible to make it more balanced and fun, crucible marks will always be the dominant currency.
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Pretty much covers it......