I think Wittenberg would be one tile west of Berlin's tile on the map (it's called Magdeburg by the city name manager). I guess it's not possible to fit it in.There is one thing i've been thinking about, not sure how doable it is, but for the sake of historical accuracy: So far we have historical holy cities in 600 AD, islam in mecca, zoroastrinism in persia, hinduism/budhism in india, etc...
But for protestantism (although the founding date could vary, as the protestant reformation lasted quite a while, there were religious wars for some time), the holy city should be Wittenberg, as it holds the All-Saints church IRL. Now I know that founding it on the exact spot would be complicated (I don't even think Lutherstadt Wittenberg is in the game), but it doesn't necesarily have to be so, it could be founded in another city, maybe in a significant city in Saxony-Anhalt (if its even in the game) or another suitable location.
I was hoping for Prussia to spawn with protestantism, (b/c, if im not mistaken, Austria is a catholic country, as was the HRE, I think it would be somewhat more historical to make prussia, besides the usual England, vikings, etc.... to be the main protestant power) but that hope was crushed by the fact that prussia would spawn in the 1700s and the protestant reformation occurred way before that.
Hopefully leoreth, being in germany, has some insight or has at least thought about this.
That said, I consider the Reformation to be more of a dynamic event, that in real history just happened to take place in Germany. Maybe if there wasn't a Martin Luther in history, Calvinism would have gained more weight, and we would be talking about putting a holy city to Geneve. The basic situation that prompted the reformation was present in nearly all European states of that time, so ingame everyone gets a chance as well. And the civ that triggers the reformation should also get its holy city, imo.
You're right that Prussia was Protestant in contrast to Catholic Austria, and I plan to make them spawn with Protestant missionaries. They come a bit late to found Protestantism, though. But maybe Sweden could be made to found it on spawn if not already founded, just like in RFCE.
It's Wien in German/AustrianIIRC Vienna (I'm done calling it Wein) is one tile from Budapest so founding it would screw up the capitals![]()

But you're right, I never thought about a Roman Aquincum. Have you already experienced what happens to the city when Germany spawns, did it disappear? I'm not sure on the exact mechanic myself.