I spend almost every free moment in Eastern Europe, have a home there, business there and a couple of bank accounts; and with the exception of Austria "Eastern Europe" is the perfect word for Americans to make themselves understood when discussing the region among themselves. If someone is offended, its their problem, not yours. There was a time when I wanted to makes sure I was polite so I did some research. Even in the United Nations, depending on the program, Hungary (for example) can be Central or Eastern Europe. The Balkans become even more complicated depending on who is defining the region. So, when I say "Eastern Europe" its just about the only term i can use and know whom ever I am talking to understands me ... and that is the purpose of language isnt it?
Anyway, back to your trip.
Two weeks is 16 days (with the following weekend built in to it). I think it could be enough time, but depends on your travel style and interests; and I think Krakow is doable for tourists, but probably not for "travelers".
AND, I have used all of the potential carriers for the Vienna - Krakow - Budapest leg, and they are all just fine.
Day 1 USA to Berlin
2 Arrive Berlin
4 Berlin to Prague (train)
7 Prague to Vienna (train)
10 Vienna to Krakow (non-stop discount airline about $100)
12 Krakow to Budapest (non-stop discount airline about $100)
16 Return home