So that's the real problem then. They need to create a faction mark currency. Faction marks, bonds, and cloaks should apply towards faction marks as well and have factions be associated with a mix of PvE and PvP, so it doesn't seem that people are trying to cheat the system to obtain faction gear.
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I have no problem with them replacing the old system with something better overall. However, I personally think they should have an improved system in place before taking the old one out. That way those who depend on the old one aren't left out in the cold.