I would stay away from the 30 years war, it would be much more suited to being a standalone mod.
Speaking of which someone is doing exactly that: The Lion and the Eagle.
As for extra factions I'd definitely have Sweden as an emerging faction, representing the collapse of the Kalmar Union. Also Burgundy and Austria are a must, if you're including Scotland then it seems weird not to include two of the most powerful nations in Europe at the time.
The problem with Burgundy I guess is how to represent the inheritance...if at all.
Maybe including the Swiss as a bastion of Calvinism?
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