There are actually quite a few long-standing unresolved threads. Like, the revivification of Princess Zulenna, who was just starting to be an interesting character at that point. Or where the Heterodyne Boys went, or where Klaus went. Or all the way back to page 3, the scary lady in the weird electromagnetic manifestation (which does resemble the time-traveling manifestations, but I don’t think we’ve seen the lady in question).
Actually, the plot as a whole is kind of stagnating, though the Foglios are good enough storytellers that they’re not really making it noticeable. Book 1, we introduce the main characters, and Agatha’s goal is to pass her classes. Book 2, we go to Castle Wulfenbach, and Agatha’s goal is to fit in on the Castle and to find her parents. Book 3, Agatha realizes she’s a Spark, escapes from Castle Wulfenbach, and “Lilith” tells her to go to Castle Heterodyne in Mechanicsburg. Book 4, Agatha meets up with the circus, and heads with them in the general direction of Mechanicsburg. Book 5, we reach Sturmvoraus territory, Agatha is captured, and the Wulfenbachs find out she’s still alive. Book 6, we have the (temporary) resolution of the situation in Sturmvoraus lands. Book 7, Agatha enters Mechanicsburg, and makes a splash. Book 8, she goes into the castle, and starts repairing it. Book 8, Agatha is repairing the castle, in preparation for everyone attacking. Book 9, Agatha is repairing the castle, in preparation for everyone attacking. Book 10, Agatha is repairing the castle, in preparation for everyone attacking. Book 11, Agatha is repairing the castle, in preparation for everyone attacking. And we’re almost to Book 12.
Up until Der Kestel, we haven’t spent more than a book or two in any single setting, but now we’ve had 4 books, going on 5, all in the same space, with basically the same pressing issue.