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[S1mancoder]

I suggest to make a ZC reward depending on how many players from that faction participate in control, making more reward for the faction with least number of scored players.

It would be like:
1) Counting total number of participants (e. g. players with score > 5) in ZC for each faction.
2) Faction with most participant get standart player ZC reward (depending on score), let it be X/score. Quantitiy of participated players from that fraction is remembered as maxParticipants.
3) All other factions will get a reward calculated as X/score * quantityModifier, where quantityModifier is:
maxParticipants/participantFromThatCurrentFaction, but no more than 5.

Example:
20 V-Tech guys capturing zone, when 6 BB's came to fight them, but got killed. 15 V-Tech guys scored, while others not, and all 6 BB's guys scored.
The V-Tech reward per score will be standart (since they have most participants, 15 against 6), while BB's will have 15/6 ~ 2.5 reward multiplier, meaning their reward will be 2.5 times as high.

Such mechanics would encourage players from least populated factions to participate in ZC, also maybe players from big factions to move to smaller. Also this mechanics can be tweaked any way, considering the idea is that the least players in ZC faction has - the better the reward.

[Myakot]

*considering the idea is that the least players in ZC faction has - the better the reward.*
If anything with such meaning will be implemented chaos will reign. Just think of a platoon of 15+ players, that'll start TK'ing everyone they see, so that they can "force" other players to join other factions and let that platoon get the juiciest possible reward. (In your case, lower chance for anyone out of the platoon to join ZC = loads of money).

[paragon]

So now people are ready to kill teammates for loot, you are afraid that they will be ready to kill for the score? I don't see much problem, because those, who wants to kill, have a reason to do it anyway. And losing gear probably more expensive than losing score because someone helped you to kill a guy.