I think the problem is the AI's decision making. Instead of intelligently deciding who to attack, they simply attack any weak targets. Even if you are the most dominate faction on earth, if your port isn't protected, you can expect the Moors or Russians to sail over and blockade it. This creates a strange world where the Turks are blockading Rome and nearly every faction is constantly excommunicated.
A cool system would be levels of aggressiveness based on factions, like Civilization III had.
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