Are there countries or areas you want to explore? I could suggest start in the Netherlands, go to Belgium for Antwerp and/Brussels, on to France to Lille and Paris, from there you could go to the South of France.
But you could also go to Berlin, Cologne or Hamburg in Germany. You can take the train to London.
Start in Vienna and go from there to Bratislava in Slovakia, Budapest in Hungary or to Prague in the Czech Republic. I might do this one next year. Vienna is one of my favourite cities and I really want to explore more. Looking at my own research it is a good hub to hop around. Also it will be a little less touristy than London, Rome or Paris.
But really, you have to narrow down what you want. Europe is huge with a many different faces and even more history. I get you are overwhelmed when all you know is "We want to go to Europe."
If you like medieval architecture go to Prague. Ancient? Rome or Athens. 1800s, go to Vienna. Etc.
What do you want to get out of your trip? When you get home what do you want to show/tell your friends and family about.
How relaxed do you want your trip to be? You have about 2 weeks, do you want to explore 1 city (and surroundings) in depth or see 10 different countries. I could make you a 2 week itinerary for the Netherlands or a 10 country trip.