Our Eastern Europe trip started in the wonderful city of Berlin. We stayed at Hotel i31 (recommended for around $100 USD/night) in the neighborhood of Mitte, which is a nice central location to everything. Transportation, shops, sights and food were all nearby.
Unfortunately we only had about two days in Berlin. I recommend staying for at least 4-6, as it's a big city with a lot to see and do. Anastasia was sick with food poisoning on the second day, so our time was even a bit more limited than planned. But thanks to excellent German pharmacies, we got the medicine she needed and were back on track by late afternoon.