Keep in mind that it's not necessarily a good idea to be trading with the enemy. The money you get from trading with other factions is negligible compared to what you would get if you, say, put 10 ships on a trading post. I consider trade agreements to be, more or less, another avenue of diplomacy. Sure, you both get a little bit of money, but in my case, it's mostly used for establishing good relations early on. It's also not so much of a good idea to trade your resources to someone that will eventually use it against you. Granted, resources don't have that much of an effect on buildings/units (thankfully), but it still opens up some potential avenues (such as Cotton for advanced Naginata, and Horses for Cavalry).
This is something you'll want to keep an eye on when setting up trade agreements later in the game. If you have 4-5 resources, you really don't want to be trading with a potential enemy, especially if that person only and already has 1 or 2 of those resources - he's getting more out of the agreement than you, because he is only providing you resources you already have, while at the same time collecting on the resources you have that he doesn't own. Free trade should really only be applied to those you want to have good and long-lasting relationships with, or if there is a resource you absolutely need. In the interim, it does provide a small diplomatic boost to an otherwise hostile clan, so it is useful for staving off potential attacks until you're ready for them - just keep in mind that caveat about trading resources.
Also, the difficulty in acquiring trade agreements later in the game is likely directly influenced by what resources they would be providing you, and also partially by how much money you'll be getting from the agreement.
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