I feel like them taking this away is setting the game up for accepting both marks for faction vendors. Crucible handler and quartermaster will probably only accept crucible marks. DeeJ did say in a recent post that there will be more use for your marks.
Have a little faith.
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I think he meant you could use those marks to buy materials. Since one could easily farm materials and get 100 an hour no one could collect that many marks in an hour. The more I think about it they screwed over both sides. What idiot would waste marks for materials when that is the easiest and quickest thing to collect? It's like paying someone in cash to stab yourself in your own hand. Much easier and cheaper to do it yourself.