Croatia Itinerary Help: Zagreb yes or no?

We stayed in Zagreb for two nights last June and had a great time. However, we flew into Zagreb. I would suggest that 1 night in Plitvice is enough. We spent 2 nights in Bosnia-Herzegovina and LOVED it! We also loved Korcula and Trogir. Back to your original question. If it was me, with the time you have and the distance between destinations, I'd probably (sadly) drop Zagreb. Btw, you didn't mention how you plan to travel. As you probably know, Croatian destinations are not well connected by rail. We LOVED our Croatian trip. Great people and a beautiful country.

The way I feel about Zagreb is that it is a pleasant, underrated city, and it can provide an interesting contrast to the coast, but I would have no regrets about leaving it out of this itinerary. Trying to include it would actually detract from your overall plan. You can always go back--it is the easiest place to fly to and could be part of a future trip to Slovenia or the Istrian part of Croatia for example.
Most people only stay a night at Plitvice (the park is definitely the main attraction and the area has limited dining options, etc.), but there are many trails that most visitors do not get to, and as an avid hiker, you may want to have time to get more extensively into the park. Check out the park website to plan in advance. The main boardwalk trails are quite crowded, so it's best to get an early start (the previous evening might be a good time to hike as well).
As to your extra two nights, many options! You could add them to existing stops, you could stop a night in Zadar or Sibenik in between Krka and Plitvice (instead of heading back to Split after Krka), you could stop on Korcula in between Hvar and Dubrovnik. I like to have at least three nights on an island. Hiking along the coast is a great way to spend a day as well--you can do this on Hvar (to Milna and take a bus back), also walking on the Pakleni islands off Hvar is nice.
Train is limited in Croatia but bus system is great. You are going at a fabulous time of year--enjoy!

I wasn't a big fan of Zagreb, so I would definitely not recommend detouring up there (about a two hour drive from Plitvice), especially given the limited time you have.. If you were passing through, or if you have plenty of extra time. I'd say it is certainly worth seeing, though.

I agree that one night in Plitvice is probably enough, if you can arrive early enough the first day to get in and hike some then and see the rest the second day. Most people can get the gist of the park in 6-8 hours I'd say, and I don't see how an avid hiker would really need a whole lot more time. It is essential to get into the park at 7am when it opens that second morning, so you have at least a few hours without the mobs of tour groups who descend on the park by mid-morning. Staying at a park hotel (overpriced for sure) might be worth doing - lets you walk right into the park.

An "avid hiker" might enjoy the much less busy Una National Park in Bosnia not far from Plitvice. It's a very different kind of experience: harder to get there and into, far less developed, though perhaps not as exotic (no waterfall at every turn, but there is one enormous waterfall). But again, you may not have time.

I'd probably rent a car if at all possible at least part of the trip, to maximize your limited time. Driving between Split and Plitvice would especially make sense if you want to stop in between - at Krka, Sibenik, Zadar, etc. Dropping the car when heading south past Split would make some sense, though. You might chop a night off of Split and see Krka when going between Plitvice and Split. You could add a day to Dubrovnik and do day trips down to say Montenegro or to Mostar. Or add another island e.g. Korcula.

We are huge Zagreb fans. If you can stick it in, by all means do. We took the bus from Zagreb to Zadar - 4 hrs, 13 €. You can get there from Plitvice easily as well.

It really depends on what you want to do. Zagreb has a good architectural/archeological museum (as does Split). It has the Croatian Naive Art Museum (featured on the RS Croatia program), which we love. It has a wonderful cemetery (which we have not gotten to in 4 trips). But you can do much of what you would get in Zagreb in Split. It has lots of restaurants and bars.

If you do want to go, you could consider
- travel from Split to Plitvice to arrive late afternoon
- do the park starting at opening the next morning
- take a bus or car to Zagreb at the end of the day (3-4 hours max)
- stay 2 nights
- take a bus to Zadar for 2 nights

As to "other cities", I would go north on the coast from Split. There is Zadar, Sibenik, Trogir. All worth a visit. 2 nights in Zadar? Sure. I don't see the Istrian Peninsula in that. You might consider 2 nights in Zadar, Rijeka, or Pula. That is still on the coast.

Thank you everyone for your kind and thorough responses! We ended up removing Zagreb from the itinerary and adding a night to Hvar and a night to Dubrovnik. Haven’t solidly decided what each of those extra days will entail, but based on advice from several of you there are hiking opportunities on Hvar and Mljet bear Dubrovnik. Thank you again everyone!