I, like most, I believe, have a love-hate relationship with this game. It's an awesome game, but losing hurts so much!
I consider it a simple game, but seeing all the simple factors interract creates a progressively complex gameplay that takes on a life on its own.
I thought the 'modding' would be merely an expansion of the game customization feature which I found to be a huge leap forward.
Right now it lets you choose an anonymous or open game, rated unrated, rating limit, factory heavy, random, generator heavy, balanced.
So, expanding this could include: Barring certain communication, barring certain or all specialists (some feel kings are OP), locked teams, choosing colors, perhaps renaming and even placing outposts. Choosing server sizes (Want to duel your friend in a huge map?), asymmetrical gameplay, custom starting or victory conditions. A game until elimination, not just territory control. A stalemate/draw by consent.
Deeper could be even changing some hardwired stats, like how many drillers are produced, how long cycles take. How many hires, how fast are the subs?
I know that arguably a game where there are no specialists, or private communication, would effectively hardly be Subterfuge... But that doesn't mean there couldn't be strategy, diplomacy.
There's strategy and diplomacy in agar.io.
These kinds of servers would have to be either classified or completely separated from the mainstream ones, because the confusion would be huge if they were all in one.
But it would put tons of power into the hands of the players. Would the know what to do with it? Some would. Maybe trends would develop, maybe the playerbase could show you something you didn't know yet.
Maybe a subterfuge game could be over in an hour, or 30 minutes.
Will you waste time in diplomacy, or just try to murder everyone while they plot against you?