Two weeks, at a sedentary pace, is two, maybe three, major cities the way I travel. That kind of limits what and where, but since you're looking at Germany and Austria your best bet is going to be either a Frankfurt/Nuremberg/Munich/Salzburg route or a Munich/Salzburg/Vienna route. (You could fly into Nuremberg, but it's limited compared to Frankfurt & Munich.)
If you chose Frankfurt you can drive the Romantic Road and see Wurzburg, Nuremberg, Rothenburg, and Munich; traveling through some of the most iconic German countryside. There are several great castles on this route (many overlooked by most tourists), lots of small, scenic towns, and good roads. I'd suggest you can easily do this in a rental car, but if you continue into Austria, go by train to Salzburg. That way there's no issue with the driving permits or dropping a car in another country.
If you prefer the Munich to Vienna route I would (again) rent a car for stuff around Munich, and then rail to Salzburg and from there to Vienna. There's not a lot of schlepping of luggage involved, and if you use a taxi to and from the train station none at all.
I'd also plan to arrive and depart via different cities. There's no major advantage to using the same airport with todays flights.
If you haven't driven in Europe before I will caution you that it is very different than the USA. Drivers are more aggressive, traffic enforcement is much stricter, and some basic habits can get you in big trouble. (For example, yellow lights are used for stopping moving traffic and letting stopped traffic know the lights will change, and they will accelerate immediately on the green. Never try to push a yellow light like is common in USA.)
Things I think you should put on your short list:
Walking through the old part of Nuremberg from the train station to the castle. You can see the city walls, the main square with the open market, the Churches, Albrech Durer's house, and a well preserved castle with a nice garden.
The towns of Rothenburg, Dinklesbuhl, and Nordlingen. All three are close, maybe 25 km apart, on the same road, and while Rothenburg gets the most tourists, the other two are just as historically important and worth walking around. If you can spare a day to each it's time well spent.
The Deutsches Museum in Munich. I love this place as it's scientific, full of neat displays, and lots of tourists miss it.
The walk along the river in Salzburg on a nice day. Everyone seems to come out for a stroll, and there's kids playing, sunbathers, ice cream vendors, etc. All in one of the most scenic towns in the world. (Look at a Luigi Kasimir etching to get an idea of the view.)
As much as I love the Vienna Opera (attend if you can) the Hofburg is the jewel I keep going back to. (If you were into shopping I'd send you to the Doretheum; Google it.)