Because there are 4 guns you can buy with vanguard marks, and 40 or so that can be bought with crucible marks. And they are useful for PVE. The faction vendors should take either/or, or the vanguard robot should change up his inventory. They are more than just different colors, they are different elements, magazine sizes, ROF, etc... And you can no longer trade mats, that is the issue.
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I got many of my crucible weapons from weekly heroics and nightfalls. I understand they have different attributes.If you play enough PVE you get the same things over time. Last time i checked the vanguard quartermaster had over a dozen which are comparable with the crucible quartermaster. the only thing that are different is faction weapons, and they are all about the same any way you slice it. This inst that big of a deal and its a non-issue.