I guess your question is too general, in terms of where to travel. Do you love to party in Berlin? or museum goer? history? classic music addict? I think the cruise down the mid-Rhein valley would be great (KD Duesseldof or others). You’ll see lots of small towns and casstles along the way. Berlin is the place to party and esp. if you are intersted in Germany’s history. You can go to the south to sample the Bavaria region like romantic road (more small town and casstles) or munich. Go to Salzburg if you like music and more casstles. Not too sure about Vienna. Innsbruck is a cool little town in Austria surrounded with the Alps, so it’s great if you like hiking in the mountains. But don’t expect any winter sports in the summer I guess. I’ve only been to Berlin and Rhein region in Germany. I wish it helps.

Yeah, pretty vague question. If you CAN go, definitely do it. There are tons of travel books out there you can look at that tell you what you should see and what isn’t worth seeing (try Rick Steves’ “Best of Europe”)
 
On a personal note though, I’d recommend Stockholm, Sweden. Kinda far away from the rest of Europe (unless you’re already in Scandinavia) but definitely worth the hassle. Beautiful clean and SAFE city.

Good choice to not overdo yourself with only two weeks.  Your question isn’t too general as you’re saying, “I don’t know much about these 2 countries, give me suggestions”  We just hate it when people spit out 5 or 6 countires and want us to plan their trip for them. 
 
I’ve flown into Germany twice, its one of the cheapest countries on the continent to fly into, but I haven’t traveled it extensively.  From what I’ve seen, I like Austria much better.  Berlin has a lot of history and a unique atmosphere, but like most of Germany, it was mostly demolished in WW2.  Austria on the other hand, especially Vienna and Salzburg, has plenty of sights that are several hundred years old. 
 
A lot of people say Vienna is a bit boring, it is a city based on classical music and museums, but there are still plenty of good sights to see.  The ringstrasse, old town section, is a unesco world heritage site and is fun to walk through.  St. Stephen’s Cathedral is an unbelievably beautiful church.  You can take a ride on the riesenrad, one of the worlds first ferris wheels, which gives a great view of the city.  Museums of anything you can think of, grave sites of Beethoven and Mozart, theaters they performed in, Hofburg Palace, there is plenty to see here. 
 
The very impressive Salzburg fortress, setting for The Sound of Music, small town charm, and the grand Alps make Salzburg a very worthwhile destination. 
 
Munich has some great history and even better beer. 
 
Prague isn’t too far away either. 

I have been in most cities of Germany.  If you are young, Berlin or Hamburg would be good cities to visit.  If you are used to a slower pace of life then get out of the cities and visit smaller towns. A nice thing about Germany is that each town has a long history with a lot to see. I always like to travel and shop in Dortmund, Hamm Münster. They arent tourist places if that is what you are looking for.  But you also will get a real since of German life.  It you want American-German Heidelberg is a city for you.