I was talking about this with HGR the other day – if the game is being totally rehauled (and thank merciful god it is), I think the big, first question that needs to be asked is what kind of game Mercenaries is supposed to be. Is it meant to be a straight-up strategy game, with different teams navigating abilities and economy and such? Is it meant to be about whose team beats whose in a fight? Is it primarily a game of backhanded political deals? Right now, we have all three, and the middle seems like it can't be combined with the other two.
The problem lies in the fact that the intention of Mercs is to be the former, via the medium of the second part, yet the overwhelmingly dominant way to achieve success is the latter. In it's current form, you cannot hope to win without making deals and forming alliances. It's just impossible. The hard part is to create a Mercenaries without the conspiracies and dodgy dealings that everyone decries.
One option I just thought of was maybe turning it into a league format? That way everyone would play everyone an equal number of times, and it makes alliances a lot harder to sustain/worthwhile.
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"Eet's game time..."