Which & How Many Cities to Stay Overnight Between Budapest & Prague?

Point to point would be cheaper. From Budapest to Prague you can either stop in Vienna and Cesky Krumlov or Bratislava and Brno.

To Vienna by train, then Cesky Krumlov by shuttle and finally Prague by shuttle is the usual trip.

I'm not a huge Vienna fan and they say Cesky Krumlov is getting a bit overly touristed (like Prague), so, if I had 6 days between the cities, I would look for a third city by discount air. Prague has a fair number of discount air connections (check the Czech Air web page as they don't always show up on the flight search engines), and Budapest has a lot of discount connections. Trick is to find one in common.

I looked, Kyiv and Warsaw and Belgrade are my favorites that are common discount airlines stops from Prague and Budapest.
With some creativity you can do things like Budapest to Warsaw by plane then train to Krakow then fly to Prague.

Budapest by train to Bratislava. From Bratislava I know a great guide for the castles and mountains of Slovakia which are stunning, especially in the winter. End the tour in Kosice from which you can fly direct to Prague. Downside is you really need a guide for the Slovakia portion. Upside, its some of the most unspoiled beautiful territory left in Europe and the Castles are amazing as are the villages and towns.

I love Kyiv too. But maybe November isnt the best time to be there. mid December to mid January yes, because that's Orthodox Christmas Season.

One night in Bratislava is fun. Personally, I think 1 night stops are the biggest time eater around. I would take the train to Vienna (make sure you choose the Austrian RailJet over the ICE...it's faster and a little nicer). The Schonbrunn Palace "outside of town" is a 1/2 day in itself. (Night #1) Then take a full day to take in the town. St. Stephen's, all the things on the Ringstrasse (Opera House, Rathaus, University, Etc.) Lunch at the Naschmarkt. TAKE THE OPERA HOUSE TOUR. Hofburg Palace, Demel's Bakery, Trzesnewski, blah, blah, blah. Point is: Vienna is AT LEAST 2 1/2 days. (Night #2/#3) Then you have two options: Take the train to Melk, rent bikes, and take the gorgeous path along the Danube to Krems taking a leisurely lunch at a vineyard along the way, OR take a day trip to quirky Bratislava. My suggestion is to take the hydrofoil boat to Bratislava (quicker downstream), and a cheap and efficient bus on the way back. That brings us to Nights #4. Then I would take a BUS (sorry, but the train SUCKS) to AMAZING Cesky Krumlov. This little village is outstanding!!! Don't let anyone tell you any different!!! Enjoy your 1/2 day once you get there, then spend Night #5, take a tour of the castle or even go river rafting the next day. I suggest the tour of the Baroque Theatre!!!! Then after Night #6, make your way to Prague.

I envy your trip. Makes me want to go, too!

A lot of folks love Vienna, so that's hard to argue. If the weather is good Cesky Krumlov can be amazing, better in the evening after the tour busses leave. I've done the theater tour and it was one of the better of these sorts of things I have done. Well worth the wait in line.

As for the train, the Railjet is at best 10 minutes faster but yes, a tad nicer. I would just get a direct train with a schedule that works with your day.

I havent been to Brno but I've seen a couple of posters here recommending a couple of days there. I think 3 nights is a little light for Prague. I only visited Vienna (2.5 days) because it was a good stop between Budapest and Prague but I liked it so much I went back a few years later for 4 full days. After reading a bit about Bratislava I decided not to day trip there from Vienna. It's hard to know what you'll like until you see it. And what one person raves about, another is bored with.

Wow, thank you all for your thoughtful responses! I tend to over-think everything and get a bit stressed out when planning things like this. This is what we are thinking at the moment:
Denver to London Heathrow, with the next day
Gatwick EasyJet to Budapest. (Flights are already booked) Will probably stay about 5 nts. in Budapest
Then we have to figure out which means of transportation to take to probably Brno and Cesky Krumlov, and another city/town that you think would be fun, (with probably about 2 nts. in each), before getting to Prague (for about 3 nts.?) Then from Prague, we are flying already booked B.A. nonstop back to London Heathrow, then back to the States the next day from LHR.

Regarding transportation, our goal is to get to each destination as fast (and enjoyable) as possible due to time constraints. Planes, trains, and buses are all fine with us, but if a "shuttle" is a van type vehicle, we don't want that for trips over an hour where we might be crammed in with 6 others.

We were going to buy the Rail Pass that you have to get before you get to Europe, but are wondering now if it's better to buy tickets for each leg, as long as we can do it kind of last minute.

Also, do you think that if we leave the USA with just the plane reservations I've mentioned, and wait to book all the direct trains/buses/etc. to the various cities, that we will still be able to get tickets at a moment's notice? We will be traveling in late Sept. to mid Oct. I worry about missing out on fast train reservations if we wait too long, if we were to choose a fast or overnight train.

Thank you all again, SO much for the help!

Susan

Another stop you might look into is Gyor. It's on the tracks halfway between Budapest and Vienna. The town center and the nearby Archabbey at Pannonhalma are the attractions. Stay at the Klastrom, a renovated 18th c. monastery.

You will pay more for train tickets if you wait to buy them, but they are still cheap and by waiting you retain flexibility.

I haven't used CK Shuttle or Bean Shuttle but they come well recommended. I can't imagine taking the train to Cesky Krumlov as it's a long trip that way.

Here are some times.

By train:
Budapest to Gyor is 1.25 hours
Gyor to Brno is 6 hours
Budapest to Brno is 4.25 hours
Brno to Cesky Krumlov is 4 hours
Brno to Prague is about 2.5 hours

Cesky Krumlov to Prague by train is 2.25 hours, by shuttle its 3 hours....

Bratislava to Brno to Prague seems to be the best trip as they all line up on the tracks from Budapest to Prague and require no great efforts.