With a POD that late, it would be very difficult to establish the German capital in a predominantly non-German city.
An idea would be to keep Bohemia in the empire: the capital in their lands could put the Czechs under control - at least one could think of that.
Another idea would be to choose Prague because first everybody back then considered it a part of Germany, but it is the only major city - besides the free cities - that is not a capital of a prince. So if Germany unites NOT under some of the great houses, one could choose Prague as a traditional capital (it was the capital once) which would not support a single prince like Vienna, Berlin or Munich would. But I think following this logic Frankfurt would still be the best choice.
So why Prague?