Definitely. We can do a Strike for 6 marks but if we take 10 minutes to do a Match we get 2 or 3 marks? Its a joke currently.
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This. My average time in a strike is about 26 minutes, but that includes weekly/nightfall and a fair amount of goofing around. More typically it takes me between 10 and 15 minutes to complete a Roc strike for 6 marks, and that's virtually guaranteed; a Crucible match takes a similar 10 to 12 minutes with 2 or 3 marks as a reward, depending mostly on the skill of my teammates (I can carry my own weight, but not much more) and the latency of my opponents. Even making estimates about time that are generous to PVP (15 minutes for a strike versus 10 minutes in the Crucible), that's 0.4 marks per minute in the Roc playlist and about 0.25 marks per minute in Clash. Reputation goes up at about the same rate but PVP generates marks at about two-thirds the rate of PVE. The OP's suggestion of 3 marks for a loss and 5 for a win would be perfect, bringing things up to just about even for me.