Best routes between countries in Eastern Europe

Are you traveling by car or by train? If by car, are you prepared to pay the very high international drop charge to avoid having to make a full loop?

What cities are you flying into and out of?

Just from looking at the map, I'd say if you're not flying round-trip (into and out of the same city), Krakow needs to be at the beginning or end. Bratislava should be between Vienna and Budapest. ViaMichelin.com tells me the drive from Krakow to Vienna is considerably faster than the drive from Krakow to Budapest, so you want to avoid traveling between Krakow and Budapest.

So by car, if you're OK with the high surcharge:

Krakow - Vienna - Bratislava - Budapest
or
Budapest - Bratislava - Vienna - Krakow.

At a glance, the longest train trip (to be avoided) would also be between Budapest and Krakow, so one of the two above routes would be best. You can check schedules on the Deutsche Bahn website.

Best is to open jaw your flights and either fly into Krakow (northern most part of your trip) and out of Budapest (basically southern most part of your itinerary) or vice versa, and take the trains from point to point. We were just in Bratislava - it is an hour from Vienna by train (make sure you go into and out of Hlavna Stanica since it is much closer to the city center and historic district) but really only worth a full day or two since you only have 14 days total. Cant speak for Krakow (yet) but Vienna and Budapest are all well worth 4-5 days each. For hotels I recommend Hotel Das Tyrol in Vienna, Hotel Devin in Bratislava, food and views from the nearby UFO Tower restaurant/bar are amazing. In Budapest we stayed at the Intercontinental because we had IHG points. Sights to see - Devin Castle outside of Bratislava, and the usual recommended sites in both Vienna and Budapest. Check out Red Pepper restaurant in Budapest (there may be more than one location - we ate at the one closer to the River and the Intercontinental Hotel).

Thank you both for your replies. Great information that has already given us food for thought.

Adding on to a lot of good advice. I've visited each of these cities, some multiple times. For me, I'd maximize my time in Vienna and Krakow. Vienna - Bratislava - Budapest are easy to do on the train. Look at Deutsche Bahn (bahn.com) to get ideas on schedules. You can select whether to start in Vienna or Budapest. I would fly to Krakow from either end. You can fly direct between Krakow and Budapest or Vienna on LOT. That would be the most efficient use of your time IMHO.

I saw a few hotel recommendations, here are a couple more:

Krakow: Seriously consider staying at the Venetian House Aparthotel (venetian-house.com). We stayed there last spring at the location was perfect. We had a room that opened onto the main square. We can't wait to go back.

Budapest: Last time we were there, we stayed at the Hotel Zenit Budapest Palace. The location is very central and wonderful for evening strolls along the waterfront.

Bratislava: If you want to stay near the old town, consider the Raddison Blu. It's older but has a cool vibe.

Vienna: I've worked and vacationed here multiple times. One of my all time favorite cities with one of my favorite hotels: The Hilton Vienna Plaza. Right on the Schottenring. Easy to walk to everything. I can't imagine visiting Vienna and not staying here.

Fly from the states to Krakow (3 nights) then fly nonstop on LOT about 1 hr flight time for about $75, to Budapest (min 4 nights), then train to Bratislava (1 night), then train to Vienna (3 nights).