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In a wonderful little game called Romance of the Three Kingdoms IX, I recall that whenever a force got too big, a few others would form a coalition against it. That sort of thing would be perfect for EU3, as such coalitions are plenty historical.
 
I also think that BB should be linked to size, rather than growth. The Ottomans, had they taken Vienna, would be a lot likelier to face opposition than, say, an Albania that had taken Greece.
 
Josephus I said:
What they really need to do is somehow work on a Giant Killer Alliance algorithim. If the human player is getting too big and has a high BB, the AI should configure 2-3 other major powers to DOW the human and form an alliance. Pretty much an extension of the BB, but more of a United Front, rather than a patchwork of individual wars.

A la the Napoleonic Wars. I've thought for some time this would be a dramatic improvement over badboy.

I would imagine it would be rather hard to implement though.