Treaty is essentially a supremacy game that got into the late game. And that is not balanced.
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It is also a game mode where you can use strategies and cards that are hardly used in supremacy, such as cattle and natives.
Its really not though. Completely different decks, played on maps built for treaty, the strategies are completely different and the gameplay is heavily focussed on artillery micro (for most civs) and booming ablities. The fighting is at a higher pace and more micro intensive also. To say its just supremacy late game is pretty naive statement.
I think the only way to balance the 2 game modes is to balance them individually. Honestly, alot of the balancing can be done with just the decks. So maybe in the future we have a “Treaty Deck” option when we create a deck that has different cards or modified cards for the mode. Hopefully in the future if the mode continues to grow, the devs might consider splitting the 2 modes up. Fingers crossed…
To balance the treaty you have to balance the imperial age, in my opinion all civilizations in the imperial age should have exactly the same powerful units and an equally strong economy, but they should also have their own customizable deck, with some cards that send great amount of mercenary or native units to break the power tie and avoid the stagnation of the game.
Another option is to make imperial age an equivalent of revolutions, but I think that would make both mechanics look uncool.
It is evident that the treaty in AOE3 was not planned, it was more of a happy accident. 
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I am not a treaty player but every game mode should have a balance of direction, supremacy other than treaty and other than deathmatch. Also, why do many team supremacy players trade treaty supremacy? Do I even see that they take treaty decks? Are they wrong or has it become fashion?