Germany/Austria Itinerary 12 days

You really need to go back to the drawing board on your itinerary. The Black Forest is in the SW portion of Germany--far from Berlin. There are many, many other more desirable places within a 2 hour drive of Munich to visit than the Black Forest.
Why don't you pick the car up as you leave Berlin and take in Dresden and Prague? Then south to Cesky Krumlov. Then south toward Linz to Hallstadt and then west to Salzburg. From Salzburg, go south into the incredibly beautiful Austrian Alps and the Innsbruck area. You're close to Fuessen when there. And you can make a circle back into Munich. Don't forget to save at least 3 days for this great city.
This is one of my favorite regions to travel through and we've toured the area a number of times.

I should start off by saying I haven't been to Berlin yet, but it is very near the top of my bucket list, and everything I read and hear from people is to allow a lot of time for Berlin and the surrounding area. So if I only had two weeks and wanted to see all those other parts of Germany and Austria, I would save Berlin for another trip.

You have a very nice loop from Munich to Rothenburg to Gengenbach to Fussen to Salzburg and back to Munich, and I think that's plenty for 14 days, but you could add a stop, perhaps Heidelberg or somewhere on the Bodensee or Innsbruck if you are so inclined. You would also have time for a day trip to Dachau if you think the kids are mature enough for that.

"We will be arriving the last few days in March... We love to walk, hike, sit and just enjoy the surroundings... Like to visit local stuff like zoos, botanical gardens, etc. ."

Chances are good that your outdoor plans will be compromised, especially in the Alps. And you are planning to cover a whole lotta miles by car when weather in the Black Forest and Alps is likely damp and cold. Not that it won't be chilly elsewhere.

I can see time in Berlin and Munich, places where you need more time than you have allotted and where you'll find indoor AND outdoor options if and when the weather cooperates. I would probably not expect any botanical gardens anywhere but zoos, sure.

To see and enjoy Germany, it is not necessary IMO to circumnavigate the whole country. Have you considered visiting places in between Berlin and Munich, or places that are sorta in between? You can find half-timbered houses - like the ones in the Black Forest - in Northern Germany as well - the German Half-timbered Road routes west of Berlin might offer what you seek. Some of the same towns are found on the German Fairy Tale Road. These towns are in very scenic areas as well.

Rothenburg isn't terribly far from some other excellent places on your way to Munich - Bamberg and Bad Windsheim spring right to mind. Besides being a beautiful and authentic medieval town and a UNESCO World Heritage site, Bamberg (like most places) offers hiking opportunities too. The outdoor Freilandmuseum in Bad Windsheim is wonderful and opens mid-March.

So I think a route like this would offer you a similar experience with a much-reduced driving regimen. More time to see Germany with your feet on the ground.

Thank you David for your alternative itinerary. Originally, we had hoped to drive through the Czech Republic, but were slightly deterred as people said driving from Germany into Czech could be expensive, so we started to question whether this was too much. But now looking at a map, your suggested itinerary helps us see Prague, and makes much more sense in terms of a road trip. It really minimizes the time between locations.

While I love the idea of seeing the Black Forest area, I see there really is a reason that people either tour Northern Germany, Western Germany, or the SouthEastern region. Its a lot of time in between.

You also suggested some areas we had not looked into yet! Very excited after reading more about Dresden.

Welcome any more thoughts and advice!

@ Russ - thanks for your reply! I did feel like we were a little "all over the place" with this itinerary. We have driven Ireland and Northern Ireland before, and that loop is so straightforward....and nothing is really too far. So planning for Germany has been a bit different, and I want to make stops that make sense. Sound like different trips for different areas some day, so as not to drive all over the place. We really do want time to sit back, relax, let kids play, and enjoy the atmosphere and culture of another country.

I'm not sure what to expect for weather, so I was going to plan as we did for Ireland in spring....and much like we would here in Colorado too. LAYERS! :) Our weather here in CO is always changing, so we plan for anything and always dress in layers. Would this be appropriate for April in Germany as well? Honestly, it has looked like it may be a bit warmer in Germany in April than we experienced in Ireland. But will pack for wet, inclement weather as well. Boots, hats, gloves, etc. Nothings worse than cold and unhappy kids. But kids who are prepared.....Will take on anything!

I agree with the earlier posters that criss-crossing Germany may be too much for two weeks. Having just been to Prague this past summer, I think your kids would enjoy that much more than perhaps some of the other places you originally had listed. Berlin, Dresden, Prague, (Salzburg?), Munich might make more sense. I don't anything about driving in the Czech Republic as I've never rented a car in Europe before. You would of course want to check the driving times between each city to see if it was worth it to spend that much of your two-week vacation driving or not. I think less time traveling is always a good thing, and you don't know what the weather is going to be like at that time of year, so you may be severely limited in outdoors activities.

We had a similar dilemma on our trip, and after some advice, changed our itinerary a bit. Seems to me that if you want to visit the black forest, you should arrive in Munich and drive from there. Then you can see much more on a more leisurely timeframe than flying all the way to Berlin and driving back south.
Having been to Berlin it is a great city, but maybe best left for another trip. There is so much to do and see in southern Germany that it would easily fill up your 14 days.

Here is an alternate to think about:
Arrive Munich, rent car.
Salburg - 2 days
Fussen - 2 days (you'll need most of one to see Neuschwanstein)
Gengenbach - 2 days
Heidelberg - 2 days
Rothenburg ob der Tauber - 2 days
Nuremberg - 2 days
Munich - 2 or 3 days
You could cut out one stop if you want to spend more time in another.
This way you will limit your driving to 1-1/2 to 2 hours between each stop, so it won't be too much of a drain on your energy or time.