Help with 13 day Croatia trip in September

First, check into dropping the car in Pula or Rovinj, then check the ferry schedule to see if it works for you. This is the one I know of, but there may be more: https://www.venezialines.com/
If that is not an option, then you'll have to sort out overland travel to Venice, and I'm sure there have been some discussions here on how to go about that. I say that because dropping the car in Venice would include a large fee. (in-country, different-location drop-offs are usually just a minor fee)
How many are you--will all of you and luggage fit in one car?
I think you have to work out the last bit before allotting nights, as you may need to get north earlier. Or, you might consider giving the south more time and flying to Venice.

It’s 3 of us with mostly just a bag each. Hence enough to fit in one car. Do you think 2 nights on each island is better than staying at one island for 3 nights and taking day trips?

Yes, three will be fine.
I'd lean toward choosing one island for a longer stay, and when it comes to Hvar vs Korcula, I usually say flip a coin--both are great.

I like your original idea to stay two nights in Korcula & Hvar, so you can experience both of them in the evening. I would be tempted to give Dubrovnik two nights, so you’re able to give Venice an extra night…unless you have already been to Venice. Or, if you want to want to keep the three nights at Dubrovnik, maybe drop one of the nights at Korcula and give it to Venice.

I looked at boat schedules and it seems I’ll need to leave 2 nights at Venice (which is awesome) but I’ll need to figure out if moving every 2 nights is worth it.

That's the conundrum! And getting to Plitvice might require a night.
Do you want to mostly tour the towns, or are you looking for beach/nature time, or ?
It is hard not to speed through when you know you have to be at the top and you are starting at the bottom, but Croatia definitely has that slow down and smell the roses kinda vibe, so it really just depends on what you all want.

I want to enjoy beach days as well as some partying. I do enjoy some hiking for viewpoints but not extreme hiking.

Then I would definitely lean toward fewer stops, as that travel time eats into chilling time. Both islands have fantastic beaches. I am not sure of the party scene dies down in September, but that is what Hvar has been known for (I was always there in May, when it was fairly sedate).

I say keep your 3 nights in Dubrovnik so that you have time to go to Lokrum Island. There is an inland lagoon there, sometimes called "the Dead Sea," and there are beaches there. It was also the site of Qarth in Game of Thrones, if that interests you. If you like kayaking, you can kayak to the island.

I love Plitvice, but it really is an outlier for your itinerary. Consider going to Krka, instead, which is not far from Split.

Also consider doing a tour to the Blue Cave from either Hvar or Split, if that interests you. If so, you will need to take a night from Korkula. In fact, I think having 3-4 nights at one island (likely Hvar, in your case) makes more sense than trying to do 2 nights each at 2 islands.

Thank you all for your help.
So far we came up with 3 nights in Dubrovnik, 3 nights in HVAR, 3 nights in split, 1 night in zadar/ pula (need to figure out ferry schedule) and 2 nights in Venice.

Alternatively we may consider flying from split to Venice and add another day to split.

Small tip.............. buy a cheap plastic float for they are expensive in Croatia. September water will still be warm and a great experience to relax using the float. Small and ez to pack and then donate upon final use.

Now, I’m already excited about laying in the water on a float.

Agree with Valdelphia and BB that if you are going to go to Plitvice, you really should plan a night there or quite near there. You'll have to reduce one of your (now) three planned 3-night stays down to 2.

Otherwise, Krka has some of the same sense of water and cascades (plus you can swim there, unlike Pitvice). Still, Plitvice really does have a very special quality.

I love your revised itinerary. Is there any particularly reason you want to visit Zadar or Pula? Stay in Rovinj so you can take the ferry to Venice.