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?