I agree with Daisi that switching to the Sapphire deck would make sense. We have done 3 cruises in rooms on this middle deck; definitely wouldn't spend the extra for an upper deck. Although we will be staying in the upper deck on our upcoming Christmas Markets cruise in December, but only because it was a free upgrade!
What time of year do you plan to sail? The Rhine and Danube were at historic low levels last month and boats couldn't sail the whole itinerary. Companies with more boats on the river (Viking, Avalon, Ama) were sometimes able to do ship swaps. Smaller companies like Emerald and Scenic might not have a 'matching' boat to swap to. Also look at how the companies treated customers affected by low water. I read several posts on an Avalon FB page that said they had to spend a night or two in a hotel instead of sailing and Avalon gave them full refunds for the days spent in the hotel, even though Avalon paid the hotel bill. While disappointed that their cruise was impacted, everyone was very happy with Avalon's customer service. I don't know how Emerald dealt with the low water because I don't follow them. But worth you looking into.