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Rouges.
By attacking anyone, does that mean you can attack the Gang(s) that have Whitelisted you?
That would be interesting.
Also, besides being mercs, they could technically become Spies, in a way. Gives an interesting dynamic to the game.
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WF Enchancements.
Yeah I don't really like the idea of mini-WL either. But something to pull in lowbies and not make them (no offence) useless would be good.
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WF Shop.
Yes please, current Shop is worthless 
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Arena.
Yes please! This sounds awesome! We could have Leaderboards and everything. A whole new competetion! There could even be banners or badges for this. Rank #1 for a Month in the Arena, etc.
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Raid System.
I still think this is familiar with Brave Frontier, and I like it. I can see this game going on the path of a full-fledged AAA MMORPG right here. ^.^
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Inventory/Hospital Revamps.
Inventory stacking, yes. More item slots, sure, but what would the Plat Upgrade do then? Even moar? 
Like rollin said, if the Hospital doesn't close, the Sanctuary would become useless.
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Crystal Levelling
More stuff with Crystals! Yay.
Maybe a Level 1 Crystal gives x% bonuses to a specific stat.
You would inlay said L1 Crystal into an item, and with every (whatever requirement it is for the item) the Crystal would get EXP as well. Same thing as the item. With every level, the stat bonus increases?
Sounds cool.
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Overall, I like the Arena and Raid ideas.
The WL Shop and Inventory ideas are a must-have.
And the Rogue system is super cool.