So maybe Johann's oldest son (Juan de Franconia?) would marry daughter of this guy:
https://en.m.wikipedia.org/wiki/Alfonso_de_Aragón,_Duque_de_Segorbe
Much younger than him, but say, that as young man Juan was too busy to marry, fighting for Spain in Italian Wars. Third generation of Valencian Hohenzollerns would be born during 1560s.
And about unequall marriage-Hohenzollerns IOTL intermarried with Croatian (Frankopan) and Lithuanian (Radziwiłł) noble families, so that marriage would not be any worse. Add the fact, that these Spanish Hohenzollerns fought for Habsburg case, they would not be denied their Franconian homeland.
The inheritance problem wouldn't be a thing during Karl V/Ferdinand I's reign. It'd be during Maximilian II/Felipe II's reign. Felipe has little to no power in the empire - and his sister, the empress, can beg, plead and protest with her husband and later sons (assuming it goes as OTL) that these Spanish Hohenzollerns be allowed to inherit, the emperor doesn't have to listen. The last time the electors of Brandenburg went extinct (with the Askaniers), the emperor (a Wittelsbach) confiscated the place
despite there being another line (the later dukes of Saxe-Wittenbergs) to inherit. Same when the Askaniers died out in Saxony. The Saxe-Lauenburgs were passed over in favour of the Wettins.
Ergo, while these Spaniards might inherit the Franconian territories (and even, perhaps, Prussia), it's no guarantee that they would get the electorate.
Weird idea came to my mind...
Johann, Viceroy of Valencia is more lucky ITTL, so to counterbalance it I'd make his Brandenburgian cousin Johann Georg, son of Joachim II, less lucky-he will die childless in 1545, Justyna before his first marriage. His younger half-brother Sigismund (1538-1566) became heir to Brandenburg, he married Sophia of Ansbach (b. 1535) niece of Viceroy Johann. Unfortunately all children from that marriage died in infancy, so after death of Elector Joachim II Brandenburg is inherited by Georg Friedrich from Franconian branch (1539-1603), who, like IOTL, dies childless. So now the only Hohenzollerns left are:
-Albrecht Friedrich, menthally ill Lutheran Duke of Prussia.
-very distant Catholic cousins from Swabian branch
-Spanish Catholic descendants of Johann and Germaine.
But's lets work with this idea: Georg Friedrich inherits the electorate in 1571. He only
married his first wife in 1579 OTL. Here, he could marry differently and beget kids. But, assuming that he or his wife are still barren, that means that by the 1590s things are going to start looking serious (is the Cleves inheritance crisis still happening on schedule? Cause then it could have interesting repercussions - especially if one of the half-Habsburg daughters of Wilhelm der Reiche of Cleves marries a son of Juan de Franconia). The Franconian/Prussian inheritance is fine, those were finalized in 1598 OTL. It's the electorate that's the problem. Brandenburg's been Protestant for a few decades by this point. When Joachim Friedrich tried to enforce a conversion to Calvinism, he came up against opposition. I have a feeling, the Brandenburger/imperial estates, are going to be even
less cooperative with a margrave who is a) a foreigner (who's probably pretty chummy with archCatholic King Felipe of Spain) and b) a Catholic. If these Franconians are anything like Karl V's kids, their Catholicism is going to be of an unbending kind (in Felipe II's case it was more pragmatic than dogmatic - Protestantism overseas was alright (if it suited his purposes - like Elizabeth of England), just not in his realm (like the 80YW in the Netherlands). Felipe III & IV were more, Protestantism bad, Spain smash (whether Spain had the finances was another matter entirely. But they didn't care); his sisters were more inflexible. Maria of Spain's comment when she returned to Spain that "she was glad to be returning to a country with no heretics" and Juana's purported being the only woman Jesuit
ever, demonstrating the more unyielding side..)