Zagreb Croatia or Mostar Bosnia Herzogovinia

If the choice is between Mostar or Zagreb I would go with Mostar and do option 2. Zagreb is a nice enough city, but I did not find it very remarkable when I was there some years ago. Mostar on the other hand has a very pretty old town down by the river and the rebuild Old Bridge is beautiful. The recent history is still very visible and it can be a poignant experience. It's also very Turkish, whereas Zagreb has a much more central European feel to it. another thin to add is that the train ride between Mostar and Sarajevo is absolutely spectacular. However I would not spend 3 nights in Mostar, you can really see everything in a few hours, so one night would be sufficient in my view. That would also give you two days to go to Plitvice. If you do that do yourself a favour and spend the night there and go to the park early before the daytrippers arrive. I was once one of those daytrippers and it was mad.

We happen to like Zagreb. It is a small city, with an upper and lower town, some nice museums, and lovely Churches. I agree that Mostar is a different vibe, but 3 nights is too long. If you went with option #1 you could see Mostar as a day trip from Dubrovnik. Either one will be a lovely vacation.

I'm one of the forum's biggest Zagreb fans, but 2 nights there won't give you a great deal of time (not counting your jetlag day) to see its many nice museums. I would certainly want to include Mostar if I was getting to Sarajevo and Dubrovnik on this trip. It will be easier to hit Zagreb on a later trip (maybe visit Ljubljana, too).

Zagreb is most certainly worth a visit - but I was not a big fan either. I think you can easily see the top museums in one day, unless you really want to spend a lot of time and soak up every bit of them. The little Croatian Museum of Naïve Art is fantastic but not big and can be seen in a few hours at most (I spent an hour, maybe less, but I'm not a "museum person.").

One night in Mostar is surely enough - I would spend more time elsewhere. If you want a detour on the way to Dubrovnik maybe detour through the Bosnian town of Trebinje - unlike Mostar with its daytime tourist crowds, Trebinje should be much more calm (I spent a night there; an interesting town for sure but perhaps not the most charming place I've been to.)

Plitvice Lakes is an amazing park and one of the top highlights of Croatia - but in the summer it will be a Disneyland-like zoo of crowds and lines after 10am. I think getting into the park first thing at 7am (stay at one of the park hotels if traveling by bus) is essential to enjoy an hour or two before it gets mobbed in the park. If that sounds like not much fun...skip the park.

Renting a car in the summer in Croatia might not be cheap, but driving is otherwise easy there (and in Bosnia too), so renting a car would add a lot more flexibility and the ability to see more places. You could have a very different itinerary: fly into Zagreb, rent a car and drive to Sarajevo and Mostar and return the car in Dubrovnik when you arrive. You could stop in some off-the-beaten-path Bosnian towns like Jajce and Travnik, both with wrecked fortresses on the hills at the top of each town. You won't see many other American tourists in either town like you will in Dubrovnik or Mostar (and to some extent, Sarajevo now). You'll find Turkish tourists in Travnik, because that was the last Ottoman capital of Bosnia. Jajce, with its huge beautiful waterfall right below the town, was the seat of the last Bosnian king I think. Anyway - this would be an option if you want to avoid the high season tourist crowds in Croatia and have a different experience than most other tourists in the summer...but by bus it would be impractical, so you'd want to rent a car.