Feasibility of itinerary

In my experience Prague takes a full three days to appreciate what it has on offer. I'm not such a fan of Budapest, but it will take two full days to take that city in.
Munich to Prague can be done on a direct train within some 5h45. Prague to Budapest is 500+ kilometres, taking the best part of a day on the train. I have no experience with private transport on this scale.
An alternative is to change Budapest for Vienna, a city always deserving a couple of days, even on revisiting. It makes travelling a lot more pleasant, especially when you can do in the order Munich-Vienna-Prague, with both legs not much more than 4 hours on the train.

Todd,
Day 1 I guess the train to Prague.

Day 2 and 3 Two full days was enough for me in Prague, but its a personal interest thing. But I would use that at a minimum. You can do the limo thing if you want, but its such an easy trip I wouldn't .

Day 4 From Prague you take Bean Shuttle in the morning to Cesky Krumlov and spend a night. I liked the Hotel Dvoark because it had a couple of rooms with a view of the castle which is stunning all lit up at night. You could skip the overnight and take their afternoon shuttle on to Vienna, but the best part of the day in Cesky is after all the day tourists have left.

Day 5 From Cesky Krumlov you take an afternoon Bean Shuttle to Vienna and spend a night.

Day 6 Vienna is always worth at least one night and it breaks up the long trip down from Prague. If you are running short of time, take a late train on into Budapest. They run all day and all night. Takes less than 3 hours.

Day 7 Take an afternoon train on into Budapest (if you didn't do it the night before. You can add this day to Prague or to Budapest. I am biased so I would say if you don't want to spend a full day in Vienna, then use the extra day for Budapest)

Day 8, 9, 10 in Budapest with 3 full days is about right

Day 11 Go home??

Not too ambitious at all.

Because the Opera is still pretty much for local consumption in Budapest they hold to the old tradition of closing for the summer.

Ten days for Prague and Budapest, including travel time between them, is fine, and will allow you to see a lot in both places and relax a bit. Adding more places will cut short some of your time in these two, which may or may not be fine for you. You may want to see a few places in more depth, or may want a "tasting platter" with more variety.

As you can see, how much time to spend in each place is very personal. I will emphasize, as I always do, that while Vienna and Budapest and Prague are spoken of a triplets, they are as different as apples, oranges, and bananas. People tend to like one or more of these and dislike others - the catch is that there is no consensus. Everyone feels differently, and you won't know how you feel until you've seen them. So read about them, watch videos on them, and decide for yourself what your priorities are.

One thing I think most will agree on is that Cesky Krumlov only needs one overnight (it's small, and nice to see when the day trippers have left, so a night is great, but there's not much to do after that).

Thanks everyone for the very helpful insights and advice.

I am realizing that I am being a bit too ambitious, as the approximately 10 days would include the 3 nights in Munich.

I guess I need to choose between either Prague or Budapest. The former seems like an easier, more direct connection from Munich, so I am leaning in that direction. Is it more touristy than Budapest? I have heard others on the board refer to it as 'Disney' version of Europe.

I tend to prefer museums, classical/opera, flea markets, wandering outdoors. Not a big foodie, especially when traveling solo. I tend to grab quick bites on my way to other things.

Todd

Logistically just in 10 days would be easier Munich - Prague -Cesky Krumlov - Munich than Munich - Budapest - Cesky Krumlov - Munich and it would also take less of your time for travel. Museums, classical, opera, flea markets are good in both cities. Wandering outdoors - Prague would be better, it's more compact and walkable and unlike Budapest has 2 medieval neighborhoods - Stare Mesto (Old Town) and Mala Strana (Little Quarters). Both cities are what I call eye candies with beautiful views across the river. In Prague from Old Town toward Hradcany Castle, in Budapest view from Pest to Buda. Prague is famous for its cheap and very good beer. In Budapest - wine. Go for Tokay. Prague gets more tourists, most of them crowding narrow streets of Old Town, medieval Charles Bridge and narrow streets of Mala Strana and of course Castle. For these localities I recommend early morning when the streets are almost empty. Budapest is more modern with wide boulevards and has somewhat Orient like feeling. The reason - for almost 100 years it was occupied by Ottoman Turks. At that time capital of Hungary was Bratislava. If I were you I would hate to drop any of these two cities unless I was coming back soon. If I had choice to choose two out of three: Munich, Prague, Budapest it would be Prague and Budapest.