The EUIV Nit-Picking about Historical inaccuracies that do and don't effect gameplay.

[Trin Tragula]

If you think something is wrong with the setup you could post a bugreport (this includes tiny stuff like ruler numbers being wrong). It may not be deemed a very high priority depending on what it is but we'll get to it eventually

If I remember right, the first Ottoman ruler in the game is named "Mehmed II Fatih", but including his nickname "Fatih" breaks the ruler numbering system so that the next Mehmed becomes Mehmed II as well.

That actually has nothing to do with why the number is wrong for future rulers. Fixed it now

 

[Trin Tragula]

The name list for future rulers has information on how many rulers of a certain name that existed before the start of the game.
In this case it wasn't updated from EU3 (which started in 1399) and thus all future Mehmets would have been number II regardless of what the 1444 ruler was named.

EDIT: Thinking on it it would probably have helped if the Fatih part wasn't there. But it should've worked anyway the way things where intended to be set up.