Chiming in here with a few thoughts.
First, what's your style? Are you energetic and fit in lots and lots every day? Do you visit a museum to see the highlights and move on? If so, I think you'll enjoy the itinerary you've set out - provided, of course, that your wife feels up to it, but that's something you won't know in advance. And if it's too fast-paced, will you be able to make adjustments? For instance, if you buy train tickets in advance, would you be able to skip the stop in Dresden? If your style is more laid back, then you're spreading yourselves too thin.
I'm all for evening train travel. I wear myself out sightseeing during the day, and then I can relax on the train, eat a picnic dinner, and then see a bit of my new destination after dark (and get oriented) before turning in.
As for individual stops, I've been to the major ones, not to the others. Berlin has first-class museums and lots of 20th century history (WWII, Soviet era) and even a lovely palace. I spent 2 nights in Dresden and loved it, but I would probably skip it with your itinerary, in favor of more time in Prague, which deserves at least 2 full days, 3 if you want a day trip to Terezin (fascinating, if you are interested in the subject). Vienna is the most Western city, it feels more like a knock-off of Paris (not by accident, either). Don't get me wrong, it's lovely, but if your emphasis is on "East" then consider spending only 2 days there. Also, if weather isn't nice, would you still want the day trip to Melk? Yes, James is prejudiced, but that doesn't mean he isn't right. Budapest deserves 3 full days at a minimum. In addition to the other sights, it has really interesting museums.