I totally understand not wanting to complicate your trip too much by adding Slovenia - just throwing it out there.
I've been to Croatia in May and in early October. September should be an excellent time to go. I think I got lucky with the weather the May I was there, because I think it usually rains more than it did that year. Going back, I'd probably pick September. Early October wasn't a terrible time, but the season was kind of ending by then, weather could still be great but turns colder at some point in the month.
I'd keep the car until Split probably. There are a few good stops south of Zadar such as Krka National Park and the lovely little town of Sibenik (Sibenik takes less time - it's right off the highway). Plus, you'l find that many rental car companies charge a one-way drop fee for short rentals. If you keep the car an extra few nights, the price may be less - even though parking in Zadar itself can be a challenge. Compare prices; maybe keeping the car until Split doesn't cost much more if anything.
I loved Dubrovnik. Yes, it's touristy especially during the day - mobbed with cruise ship tour groups. At night, it gets less crowded, and it's magical. Best place to watch the sunset: the Buza Bar!
Dubrovnik is a good place to get away from during the day and do day trips out - but at night, great place. Three nights makes more sense if you are flying out of there; your last night might be early, ready to pack up and go home, so three nights may not be all that much time.
I spent two nights in Zagreb. One night would have been enough. I'm glad I visited, but after half a day I was done - wished I'd picked up the rental car and headed to Plitvice a day early.
But it's all a matter of taste and preference. I know some people love Zagreb more than I do - some don't appreciate the beauty of Dubrovnik that I found despite all the tourists. (I know you still found it beautiful, James - some don't.) That's the dilemma for people planning a trip: which places will I like and which ones not? They have to try to weigh the feedback of different travelers based on their own preferences. Always part of the challenge of planning a trip!