Best Italian city for 3 days?

My fiance and I are going on our honeymoon this summer. We will be spending four or five days in Munich, Germany and four or five days in Zadar, Croatia. In between those two cities we would like to spend three days in an Italian city. We will be travelling into Italy, during the last couple days of July.

I am a history buff, so Rome seems like a good option, but with the crowds and begining of holiday, we wonder if it is worth it. Otherwise Florence or Venice seem like good possibilities, but all seem overcrowded and over touristy. What's our best option? Or should we skip all this Italian business all together?

After the Italian city, we plan to take a bus to Ancona, Italy and from there ferry over to Zadar, Croatia.
Additional Details
Thanks Venice is on the way by train, but we are hoping to fly from Munich to the Italian city. Does anyone know a website for cheap flights to Rome, Venice or Italy?

Thanks for all your great responses. No one has said much about the crowds as a problem, but I guess that comes with the territory.