Most of these ideas I like but I have some comments.
I think the name changes to Most Serene Duchy of Venice or the Duchy of Venice, not sure though.
If the game was expanded to include the 19th century (which I don't see happening in a very long time) then would you think it would be a good idea to make the Teutonic Order and Prussia separate civilizations?
There is already a thread on this page covering this and I don't think it's that far of a scroll down. It deals with some major changes concerning the Papal States and the ideas there will probably be implemented into 2.0 I'm guessing (or I hope).
In my game I didn't see Venice's change from Republic, but I'll look again. And the change from the Teutonic Order to Prussia is best represented by a civic or religion change. Historically, the Teutonic Order changed to the Duchy (and later Kingdom) of Prussia when they converted to Protestantism, so maybe that might be a good way to model the change. Of course, this is based off of the hypothetical scenario that the game is expanded.