We just returned from our Viking Danube cruise, Budapest to Nuremberg, October 5-12. We were notified we would not be leaving from Budapest about 2 days before the cruise started. As we were already in Budapest (2 nights on our own) we were asked to come to the Viking Idun, moored in Budapest, the afternoon of embarkation. Viking took our luggage and we boarded the Idun for a nice buffet lunch. We left by bus around 3 pm and embarked our ship in Komarom, Hungary. So we missed late afternoon/evening in Budapest on the boat. Viking bused everyone back to Budapest the next morning for the included excursion but we skipped it as we did not want to spend more time on the bus and we had seen some of Budapest on our own. We walked around Komorom and crossed the bridge to Slovakia to walk around. The boat was moored near the police station and was not scenic but we had a good laugh about that.
Day 2 (after Budapest excursion returned) we left for Vienna. We did the included excursion of Vienna (walking tour by subway, very good) and walked around after. The boat did not leave Vienna until midnight, allowing late evening excursions to return.
From Vienna, we moved to Krems/LInz. Toured the Gottweig Abbey and cruised the Wachau Valley (yes, the boat cruised the whole thing).
From Krems /Linz we moved to Straubing, Germany and a ship swap. Bused to Passau from Viking Var for walking tour, organ concert, and lunch in Passau. Bused back to different boat, Vking Tor, at 2:45 or 5 pm (passenger's choice) in Staubing, Germany (middle of nowhere but quite pretty with a lovely sunset). Moved to Regensburg at night, moored in town.
Regensburg walking tour (very good), ship leaves just after lunch. Some passengers stayed in Regensburg for the afternoon and a bus transferred them to the boat at Kelheim (we stopped only to pick up passengers). Moved on to Nuremberg, moored just outside of town, bused in to town for tours.
All in all, I think Viking did a good job dealing with unusual water and weather conditions. The key is flexibility! Given our experience and what I now know about river cruises, I don't think I would book private excursions during the cruise. There is just too much variability as to what may happen when on the river. Anyway, I feel lucky we got to cruise as much as we did - even with the ship swap (which was fine by the way) during this hot and dry year on the river.