Prebook activities? or Pay as you go?
Not sure what you mean by "activities". Day-trips (bus tours, etc.) usually have to be booked in advance. I took a once-a-week tour called "Inland Istria". I'm not aware of any museums or other traditional sights in Croatia that require advance-purchase of tickets, though there may be a few.
Plitvice Lakes National Park was utterly overrun during day-tripping hours at the time of my summer 2015 visit. There was an hour-long ticket line, but even if you had a prepurchased ticket, you would still have run up against packed walkways inside the park. A better solution there is to stay in or near the park the night before your visit so you can enter around the time the park opens.
Yes, Plitvice was crowded (just there, less than 2 weeks ago). So is Yosemite. There are reasons for that.
We walked close to 8 miles through Plitvice Lakes and saw absolutely no litter. Just lots of little waterfalls (and one really big one).
At this stage in the season you can probably pay as you go, as the queues shouldn't be too long / everywhere shouldn't be too crowded. DO make sure you check the places you want to go to are open though - many close in mid October...