I don't know what a shuttle-plus-tour entails, but let me give you some ideas. Personally, I'd rent a car.
(It always puzzles me why folks recommend making the detour to Hallstadt when advising on sights from Vienna to the Czech Republic. Hallstadt is close to Salzburg, but is most easily reached by car. And going there takes you at least 80 mi. out of the way, so the region of Salzkammergut that Hallstadt is in is best visited on the way to Salzburg).
There are lots of picturesque towns and natural areas on the route. Other than Melk, there is Dürnstein with its wine tradition and the fortress on the hill overlooking the Danube. If you are headed directly to Cesky Krumlov/Krumau, then there is the Waldviertel region to savor on the way to Zwettl with its lovely monastery. Several castles to view, incl. the Renaissance Rosenau Castle on the way west. Mauthausen is a favorite stop for Steves' travelers, but you have to get off the train in Enns and then across the Danube. Car and bus are the only way to the former concentration camp. Austria's third-largest city, Linz, is often overlooked but the city square, the Roman castel overlooking it, and the ride with an old cog railroad to the pilgrimage church on the Pöstlingberg just across the river are all commendable.
Virtually a must-see for tourists is the walled city of Freistadt, which is on the way to Cesky Krumlov/Krumau. Its medieval and baroque town center, fortifications, the interesting museum in the fortress tower, and - highly recommended - one of the finest pastry shops in Austria (Lubinger's) is right next door.
As a native of the region, I can recommend that the entire Mühlviertel (the Austrian quarter north of the Danube) is worth exploring. There is a tourist website (www.sterngartl.at) that can give travelers a good insight in this hillcountry full of picturesque towns. Feel comfortable in taking the side roads - you'll meet the rest of the Rick Steves throng 40 mi. north in Bohemia anyway!