It may be too late for you now, but we visit in August. Two of us are flying on Germanwings, taking the evening flight at 9:15 pm to Stuttgart, spending the night at a hotel close to airport, and taking the morning flight to Krakow, arriving at noon. The price was reasonable, I think about $250 for 2 of us, maybe less (I booked several months ahead, hence price). Originally we were scheduled for an early morning flight, but that was eliminated. Since we had already booked it, Germanwings paid for our hotel in Stuttgart. All other flights took too long or were too expensive. The overnight train was not guaranteed to have electrical plugs, and my husband needs for sleep apnea. I wanted to minimize the time traveling around Europe, so we are using budget airlines rather than the train. I love the train, but in 16 days, the idea of giving up 5 days traveling around on 10-14 hour rides didn't sound appealing.