joannebrewer, I've been to Croatia twice in early October, including just last October.
The weather can be warm and sunny if you are lucky, but it's also possible you'll get big rain storms and chilly, windy weather. It may not be gradual - just warm a few days, then a storm comes in and suddenly it's colder and wet...then maybe warm again a few days later. Obviously it varies a little every year. Last fall, I delayed my arrival into Split by a few days because the last few days of September, they were getting hammered by rain (and I had already been through that in Split once!). By the time I arrived October 2, I had great weather for the next day days in Croatia and later Slovenia - not a single drop of rain. It was warm enough to swim (but not that warm) if I wanted to - I did a few times. Not many others were swimming. Once I got in the water, it was fine.
I don't know what your interests are. Apparently you like national parks, so that's fine. Plitvice is amazing. I didn't see all of Krka, just the huge cascading waterfall, Skradinski Buk. If you're into parks then it's worth your time to spend time there, but I wasn't interested in spending a night - just spent a few hours at the big waterfall, walking up and around it.
Pula and Zadar both have some Roman ruins, but I wasn't really that excited about them. (I'd been to Rome and Pompeii.) Again, if those things interest you, go for it. Zadar was not my favorite town - it was nice, but one night there was plenty. I much preferred the town of Sibenik, which was much less touristy (I spent only a few hours there not a night). SIbenik would make a good base for Krka - it's not far from the park.
Some people are excited by the islands. I finally explored Hvar as well as Brac and Vis on this trip (saw Korcula years earlier). The islands are definitely slowing down by early October. I did day trips from Split to Hvar, Brac, and Vis. Hvar Town was beautiful but seemed too upscale for my tastes. (Would probably have the most going on in October for an island.) Supetar (Brac) was very pleasant but seemed ordinary compared to Hvar. But Vis (town) was somehow amazing - hard to explain why, but I really fell in love with it. So after a quick day trip from Split, I came back for two more nights. Since it was October, it was pretty slow, but restaurants were open, and that's where I went swimming. (If you like cats, there some very friendly strays on all the islands, especially on Vis.)
Unless you are dying to see the old Roman amphitheater in Pula, I'd probably skip it and add a few more nights on islands. (If you want to go to Istria, consider the charming little town of Rovinj instead of Pula.) You might also consider being flexible in your schedule since it might rain and you might want to re-arrange. Things would be slow enough in October that you could wait until the last minute to book things, except your arrival and departure hotels as the beginning/end of the trip. (If you have a smart phone, very easy to book with sites like Booking.com.) E.g. if it's going to rain for the days you had planned for islands, but the weather will clear up later, maybe re-arrange. Have alternative places to consider like Mostar, Bosnia, instead of the islands if the weather is poor. Don't lock yourself into places where the hotels are non-refundable if enjoying them is dependent on the weather. I doubt I would have gone to Vis if it had been rainy and windy.
I didn't rent a car this last trip - just took ferries, trains, buses. Last time I rented with Oryx. Before that, I used Sixt. Any of them are probably OK - be sure to get insurance to cover car damage, don't rely on your credit card for insurance coverage.