But you just gave the historical reason: forming Franconia was an ambition of several rulers in the EU4 timeframe. Albrecht Achilles of Brandenburg-Ansbach waged war against Nürnberg in 1449 exactly with the goal of reviving the Duchy in mind. Had Albrecht won that war, of course, it would not have been a given for the Emperor to grant that duchy or the other princes of the HRE to recognized his claim, but it would certainly have been possible.
Also, Bernhard von Sachsen-Weimar was actually promised the title of Duke of Franconia by Gustavus Adolphus, and had the title bestowed upon him by Oxenstierna in 1633.
A Duchy of Franconia is less fantasy and less anachronistic for the EU4 timeframe than, say, Romania, Italy or Germany - which is not to say that there are not many more important countries to be added. Just as an example, it would be much, much, much more crucial for an accurate representation of the Franconian region to have an independent Bamberg.
EDIT: As a reply to Sagif: you probably misunderstood the suggestion. Franconia would be a formable country and it would not exist at any startdate except maybe between 1633 and 1635 as a Swedish vassal, if we want to represent Bernhard von Sachsen-Weimar (which would be kinda cool).