Is Plitivice Lakes a "must-see" as far as views/hiking goes? We would really like to go there, but I have seen some pictures of the crowds there during peak season and I'm not sure if I want to deal with the volume of people in that type of area. Maybe mid-to-late September would be thinner? We could fly into Split and back through Dubrovnik, or in and out through Dubrovnik, as I believe most of what we would like to do is focused on the southern half of Croatia.
I have no doubt that mid-September will be less crowded than peak season, but don't expect an empty place mid-day, if your plan is to stop on the way from Zagreb to Zadar. As a few of us have said (maybe in other threads), it's really best to stay over at or near Plitvice so you can get into the park first thing when it opens so you have an hour or two without so many people. (I think it will still open at 7am in September.) FYI, you can see the gist of the park easily in 6-8 hours.
"Must-see?" That's a relative question that depends on one's perspective. Is ANYTHING in Croatia really a "must-see?" Not sure, but I found Plitvice one of the highlights for sure. (Zadar wasn't for me personally.) I found Plitvice amazing - I've been twice on two different trips. I am not an avid hiker, but I am an avid photographer, and the views were unique for me, the photo ops seemingly endless. And I live near some amazing waterfalls here in the Pacific Northwest.
As far as hikes go, I wouldn't rank Plitvice tops. It's a highly developed park with man-made boardwalks. I think my favorite hikes have been in the Italian Riviera. But the scenery at Plitvice is tops in my opinion. Still, I'd NEVER go in the summer mid-day with all the mobs of people. I'd go slightly off season (May or early October were my two visits) and try to enter the park when it opens or hike at the end of the day after tour groups have left. Mid-say in September will still not be uncrowded.
If you can't stay over, what do you really have to lose by stopping for a few hours besides the park fees? An extra night between Split and Dubrovnik because you've started in Split not in Zagreb? Dubrovnik will probably be mobbed with tourists, too, no better than Plitvice. Croatia is no longer undiscovered.