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The solution we chose in the Great Game was to make Germany, France, and Byz AI, and permit players to take duchies in those countries. If Brandenburg wants to become independent, it can fight for the privilege. Which indeed happened, and they lost.
A solution to the Germany problem could be to remove the Kingdoms of Germany/Italy from the province setup, so that once the vassals go independent, they wont just pledge allegiance again later on. At least I think it is possible to mod . Those countries that we do not really want to see in EU2 could be removed completely, while others, that we just want to make less über (France, England), could have their area of influence reduced.
Another option would be to start with Byak's Many Kings, Independent Dukes mod (bad name.. should be NO kings, Independent Dukes ) I've had more fun playing it (SP) than other mod (either CK or EU). Everyone starts as a Duke, there are no kings, lots of claimable kingdoms, etc. It works with the current patch. Even the AI seems to like it