Which is the better tour? I welcome you're feedback.
We took this tour last year when you could do both (longer itinerary then). Both are pretty towns, Chesky Krumlov is maybe a little more attractive. The highlight of Passau is the organ concert and baroque cathedral. We also got a candy making demonstration there, not sure if they still do that. In Chesky Krumlov, the highlight is the castle (complete with a rather mangy bear in the moat) and gardens. We got a gala buffet lunch there with costumed medieval entertainment. Judging by the new itinerary, you won't get that. If it were me, I'd go to Chesky Krumlov and try to see a little of Passau on your own if time allows. But, if you like organ music, the organ concert is really worthwhile. Too bad you can't do both.
We have been to both on separate non-Tauck trips. Both are very, very interesting. However, if you have any mobility difficulties, both can be somewhat challenging. In Cesky Krumlov we started at the top of the of the steep hill leading through parts of the castle down to the very, very attractive town. It's a long way down. Once in the very, very interesting town we had to lunch on our own and had monetary problems since most places didn't accept credit cards and we had no Czech money and Euros weren't welcomed. Afterwards, there was a very long walk back to the bus parking lot. Tauck may handle that better. I don't know. In Passau there is one fairly steep hill to climb from the place where the boats dock to the cathedral, but it's certainly manageable if you can take your time. As others have said, the cathedral is beautiful and the organ concert is lovely. Much of my reply applies only to those with some mobility difficulties. My fully able husband helped not only me but also others with similar problems.
Regarding lovestravels comments: In Chesky Krumlov, Tauck drops you off at the bus parking lot (probably the one that she ended at) and picks you up near the gardens of the castle (probably where she started). All of this is subject to change, since they have changed the tour this year. From the bus parking, you walk down to the bridge across the river then up to the castle. Steep uphill to the castle and a fair number of stairs in the castle and gardens (as I recall). However, you have lots of time to wander and make your way up the hill, so it should be a problem unless you have a mobility issue.