Road trip route through Southern Germany, Austria and Switzerland

You could fly into Vienna and enjoy the city and pickup the car on your way out. Head west to Hallstadt, Salzburg and then go south into the Austrian Alps toward Innsbruck. The mountain scenery in Tirol is absolutely incredible, and we find Austria much cheaper and easier to travel to (than Switzerland).

If after June and the snow melts, you could take the Grossglockner High Alpine Highway south of Zell-am-Zee--which ends down on the Italian border and is the most beautiful place I've ever seen. Then take in the Dolomites before heading back north thru the Brenner Pass into Austria. If time permitted, you could even see Venice.
Drop the car in Innsbruck and take the train back to Munich--another very interesting city for teenagers. It's worthy of 4 days. Then fly home from there.

Than you for this input. Are you suggesting I should skip Switzerland and southern Germany (besides Munich) and opt instead for northern Italy?

I'd fly to Geneva. See what you want in Switzerland and then head to Vienna and fly home from there.

My advice for narrowing down what to see is pick the three things you absolutely need to see or do and plan around those. To me two weeks is barely enough time to see the three cities you mentioned, and that's not leaving much time for anything else. If you did Geneva, Bern, Zurich, Lindau, Munich, Salzberg, Linz, and Vienna you'd have two days each and that's not much. But it would be a really nice trip.

I would leave Geneva out. Fly into Vienna and after visiting there make stops you want on your way to Salzburg, do Salzburg, and then head to Munich and enjoy before flying out from there. I really liked Hallstatt and its' Salt Mine but there are a lot of other places between Vienna and Salzburg.

After a bit more research on flights and car rentals. I think I need to rent a car and fly in and out of Munich. It's the only feasable ($) option. I like the idea of ditching Geneva. Maybe Munich - Zurich - Innsbruck - Salzburg- Vienna -Munich. How does that route sound?

You definitely don't want to rent the car in one country and return in another. It's quite costly. A car is a burden in cities. Is your goal just to be in 3 countries, or are those particular cities of major interest to you? Two weeks sounds like a long time, but in reality it's not. If you spend 2 nights somewhere it equals only one full day, 3 nights is 2 days, and so on. If you try to cram too much, the trip will just be a drive by of places that you won't remember later. Be realistic about what you can really see. I suggest flying into Vienna. Pick up your car as you leave. See the beautiful (and less expensive) countryside in Austria. Salzburg is definitely worth a visit. You could finish up in Bavaria by seeing the Garmisch-Partenkirchen/Mittenwald area if you have time. Return the car in Reutte (Austria) and train to Munich. If not enough time for that you could return the car in Innsbruck and train to Munich. Fly home from there.

Two problems with your suggested route:
1) As Andrea says, hiring a car in one country and returning it in another usually has a large surcharge. Return it in the same country you hired it, not necessarily in the same place.
2) A car is good for rural areas, a liability for cities, yet you say "main stops on the route would be Munich, Vienna and Geneva.". You do not want a car when you are there.

Plus, why Geneva? That is not high on the list of places to visit in Switzerland, the best places are in the mountains.

What I would suggest is, fly into Vienna, spend 2-3 nights there and pick up your car on the way out of Vienna.
Do a loop through Austria and Bavaria visiting small locations, no time for Switzerland.
Return car in Salzburg (Austria), one night there.
Train to Munich, 2-3 nights there, fly home from Munich.
That will still be rushed, but gives you your road trip.

Maybe Munich - Zurich - Innsbruck - Salzburg- Vienna -Munich. How does that route sound?

Again, all cities for which a car is a liability.
Skip Zürich, same argument as Geneva, not in the mountains, and you can't drive in the city.
Munich to Switzerland is a long and slow route.

Munich - Innsbruck - Salzburg - Vienna - Munich is a good loop by train. With a car, choose smaller places.
You need to research places in southern Bavaria, for example Oberstdorf (my favourite), Garmisch-Partenkirchen, Ehrwald and any more.

When I took my sons to Europe, I asked them what they wanted to see. "Castles". I asked whether they preferred restored castles or ruins. "Ruins". So my itinerary included both Rheinfels and Ehrenburg ruins, as well as restored castles.

I think you're missing out not planning at least some of the Rhine and a medieval town, or two, on the Romantic Road. I like Bacharach on the Rhine, the KD Line boat between Bacharach and St. Goar, as well as the Rheinfels ruins. Our kids enjoyed the night watchman's tour in Rotenburg. My favorite Romantic Road town is Wuertzburg because it has a Bishop's Palace and Castle.

I really enjoy Salzburg and Munich but found Innsbruck isn't worth much time (unless as a base for skiing). Hall in Tirol (next door to Innsbruck) is worth a short look.

We enjoyed the Salt Mines in Berchtesgaden, as a day trip from Salzburg, but clouds obscured the views so it wasn't scenic at all.

The high mountain trails (and some roads) won't really be open until later in June in Switzerland. The mountain views may be obscured by clouds. Without the mountain trails, small alpine villages and views, Switzerland offers hyper-expensive cities. If you can, have a plan B. Don't spend a lot of time and money in Switzerland if you won't be able to experience your favorites. No sense blowing your budget if you can't enjoy it.