Option 1 is self explanatory
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Option 2 - Allow players to exchange Vanguard Marks for Crucible Marks, or Vice-versa.
Changing one mark to the other counts towards the new Mark's weekly cap, so if you run a Tiger Strike and get 3 Vanguard Marks, then change them to Crucible Marks, you now have 3/100 Vanguards for the week and 3/100 Crucible for the week, without ever setting foot in the Crucible
Exchanging would not effect Reputation, so you still have to run the normal activities/bounties to rank up.
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Option 3 - Introduce a Faction Currency, an Item like Strange Coin(s) or Mote of Light.
Possible exchange rate of 10:1 (Marks : Faction Currency). Weapons would cost 15 and Armor would cost 7 (150 and 70 Marks equivalent)
This would also allow players who run multiple characters working up multiple factions to more easily buy Faction Items, provided they have the required rank with that faction.
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[spoiler]If this gets enough likes, replies, and votes, maybe DeeJ will see it and be able to pass the more popular ideas up the chain[/spoiler]