How to choose the best itinerary for Croatia

Lots of 2 night stays. Those translate to 1 day of travel, 1 day of tourism.

Much as I love Ljubljana, I'd drop it.

I'd do this:

1-2: Dubrovnik
3-5: Split, using catamaran to travel
6-8: Rovinj
9: Plitvice - stay over night, tour park in morning first thing, drive to Zagreb
10-11: Zagreb

Personally, I'd drop Rovinj, add a night in Dubrovnik, ad a night in Split, do day trips from each to Cavtat (D) and Trogir (S).

Another approach is to add back Ljub (2 nights), eliminate Rovinj, and try for 3 nights in most places.

I wouldn't do both Ljubljana and Rovinj. One or the other. Rovinj is a lovely little town, but it's not really a destination. It's small, and you can explore it in just a few hours. It makes a great base for exploring the area, and two nights isn't really enough to do that. Three nights would give you a chance to explore the Istrian hill towns, explore Roman ruins in Pula, and come back to charming Rovinj at night, without rushing around so much.

Or do three nights in Ljubljana (or two plus two in Zagreb). Ljubljana is maybe my favorite city in Europe: charming and vibrant but still not as overrun with tourists as everywhere else.

Another option would be to skip both Rovinj and Slovenia. Do Dubrovnik, Split, Plitvice, and Zagreb, but add more stops along the way: maybe a stop/detour to Mostar, Bosnia or a few nights on one of the islands like Korcula or Hvar. (The island tourist traffic really slows down in October, though, when I visited Korcula a few years ago. Restaurants were open in mid-October but it was pretty dead in town.) You could stop on the way north in places like Krka National Park and nearby Sibenik, a lovely town; in Zadar a town some people really love (though I didn't).

The one benefit of doing inland cities at the end (Ljubljana and Zagreb) is that it may be raining by then. The weather will probably turn colder sometime in October, maybe more rainy. Do you want to be in a small coastal town in the rain, or would you rather be in a larger town/city with museums, more of a restaurant scene, etc.? Of course, the weather may be warm and beautiful the whole time - who knows? On my October trip to Croatia a few years ago, I had great warm weather in Dubrovnik, but the day I left for Korcula, the rains came in and it cooled down a lot, and I had to deal with a mix of sun and torrential downpours the rest of my time in Korcula and Split. But...that was one year! Maybe not this year.

Even better, you might consider just winging it: plan nothing north of Split except your last night(s) in Zagreb. (If it's going to pour rain on your planned day at Plitvice, is it really worth doing? But maybe a few days earlier or later - ?) It's not hard to book stuff last minute in Croatia off season if you have a phone or tablet or laptop with you. I did a "wing it" trip to Croatia a few years ago (in May) where I booked almost nothing more than a day in advance and adjusted my itinerary day to day. In your case, if you are enjoying Split, you can stay an extra day; if you are having great weather, stay on the coast and skip Ljubljana, but if it's gotten rainy, ditch the coast and head to Ljubljana and Zagreb. It can be exciting to travel spontaneously like that, and it's not very risky in modern times with smart phones etc. to book things as you go along.

First I have to ask about you--do you typically travel this way and like it? I hate lots of one and two night stays, but you should plan your trip according to your interests and preferences. But you did ask, so you already must have a feeling it is too much. I would eliminate Rovinj and Ljubljana so you can have at least three nights somewhere. Although Istria is nice for October with truffle festivals and such, since you are coming from the south and the departure is set, I would focus on Dalmatia and save Istria and Slovenia for a future trip.
The islands get quiet in late October, but in early to mid October I would include an island, or you could consider popping into Bosnia, or use the car to explore Paklenica park near Zadar before heading to Plitvice.
Time in Split depends on what you want to see and do--you can see the palace in an afternoon and move on, or you could settle in for longer and do some day trips.

I would drop Rovinj as I think it's the most out of your way. I'd go from Kotor to Dubrovnik to Split to Plitvice to Ljubljana to Zagreb. You don't really need a car in Dubrovnik or Split, so I'd rent it in Split and return it upon arrival in Zagreb. You could visit Lake Bled or one of the caves on your drive to Ljubljana, although they would be a slight detour. I'd add one of the Rovinj nights to Ljubljana and the other to either Split (day trip to an island or Trogir) or Zagreb (sightseeing). Be aware that you must buy a vignette to legally drive on expressways in Slovenia, and the fines for not having one are quite severe.

As others have mentioned, your pace is fast with several changes of hotel, but that may be the way you prefer to travel. If not, then consider eliminating both Rovinj and Ljubljana and adding more nights to your other destinations.

Thank you for all your replies. I appreciate all the information. I am going to drop Rovinj from the itinerary and add the 2 nights to Ljubljana and Zagreb. The only other thought is to also skip Ljubljana and add more nights to Split. I like the idea of winging it depending on the weather but not sure if that is in my comfort zone. If we do not rent a car till we get to Split what is the best way to get from Dubrovnik to Split? Thanks again for all your help.

Between Split and Dubrovnik you have frequent buses, takes about 4 hours. Or you can stop over on an island en route but service becomes less frequent in October. The two operators are Krilo and Jadrolinija so you can check schedules to have an idea just in case. There is also a bus from Dubrovnik to Mostar and Mostar to Split if you wanted to stop a night.
In October, things should not be booked up. I'd put a booking app on your phone just in case for flexibility.

The drive from Plitvice to Rovinj is long and tiring given also that the road is not a highway.

Not sure what you mean. Most of the drive is highway as far as I can tell. I have never driven it directly, but I have driven most of it in pieces. The road from Rovinj to Rijeka is the two lane "express" Ipsilon, a toll road. Most of the drive to Plitvice from there is a highway, though you have to get off the highway to a two lane road to get to Plitvice at the end. When I drove from Rijeka to Zadar a few years ago on the highway, I could have gotten off to detour to Plitvice on the way down.

Well, I guess we will have to agree to disagree, because I have driven the Ipsilon between Rovinj and Rijeka, and it is a restricted access road (with tolls) even if it is only two lanes. I drove it partly at night. I remember it being a nice road.