That's less of a flaw and more like the premise of the game really. The clue is in the title, Total War. The aim of the game is to conquer the world. I don't mind if they make it a little harder to do so, but I don't think the game would be as good if you couldn't.
I doubt they will ever 'fix' that paticular part of the game, because there are many people who don't regard it as a problem.
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