What other sites of interest in Germany (besides the Castle Church [Wittenberg] and the Pergamon Museum) will be undergoing renovation in 2016? We are likely to visit Heidelberg, Worms, Mainz, Munster, Eisenach, Erfurt, Leipzig, Wittenberg, Berlin, and Potsdam.
Are you asking about important sites in the entire country of Germany?? Also by Castle Church do you mean the Schlosskirche in Wittenberg or another city? There are several "Castle Churches" in Germany.
People on this forum might have a better chance of helping you if you list the places you'll be going to in Germany and what are your must see sites.
Also, we've learned to just accept scaffolding at about 10-25% of the sites we visit therefore if we show up and there isn't scaffolding, we're happy.
If you make it as far south as Munich, the marvelous Deutsches Museum is now undergoing a ten-year renovation project, causing about half of the major exhibits to be closed. Aircraft, with the exception of the large Junkers Ju.52, have been or are being moved to Flugwerft Schleißheim for display.
Check for updates to your guidebook:
https://www.ricksteves.com/europe/germany/guidebook-updates
Like the others said, just expect renovation here and there as a fact of life. Particularly in the old DDR, where historic preservation received less of a priority than in the west.
Allow me to make a few suggestions. Near Wittenberg, give yourself a few hours to check out the magnificent Garden Realm of Würlitz. It's extremely close.
Worms has a very long history, but little of it besides the cathedral and the old Rhine bridge can be seen today, because the city now mostly consists of post-war modern reconstruction. Speyer just down the road also has a massive Romanesque cathedral, but unlike Worms, it was barely touched in the war. Unless you have some particular reason to visit Worms, I would give Speyer higher priority.