I haven't traveled that specific route recently, but I can tell you that one advantage of the bus is that it takes you to the Zagreb bus station (naturally), which is your departure point for the ride to Plitvice. Although Zagreb's bus and train stations look quite close together on a map, it takes a fair amount of time to walk betwen them--maybe 15 or 20 minutes, I would guess.
The bus station in Zagreb is much more heavily used than the train station. There always seems to be a line of taxis at the bus station; I'm not certain you can count on that at the train station. The city has a good bus/tram network, but I don't know how frequent service is between the RR station and the bus station or how far you'd need to walk to get to the appropriate stop. Nor do I know whether you can pay on board or would need to buy a local-transit ticket before boarding.
I don't know whether you're planning to buy your Zagreb-Plitvice bus tickets in advance. I've never done that online so don't know how well it works.
As of 2015 the ticket windows at the Zagreb station were upstairs, and finding your way to the correct platform at ground level wasn't a trivial matter. (Also, there was an up escalator but no down escalator. I didn't notice an elevator, though there may be one.) Multiple companies making the run to Plitvice somewhat complicated matters. On the other hand, service was pretty frequent during my midsummer visit.
I encountered a bit of a line at the ticket window and was afraid of missing the bus I wanted to take. A bus-company employee told me I could buy my ticket on the bus at no additional cost. The first part was true; I'm nearly certain the second part was not, but the fare difference was not large, and there was space for me on the bus. I cannot guarantee that that technique would work for you.
For what it's worth, I found Croatian inter-city buses to be comfortable.
I assume you are planning to see the bulk of the park on Sunday, after spending Saturday night in the Plitvice area. Day-tripping to the park yields the worst possible conditions (massively crowded walkways), and weekends are probably considerably worse than weekdays, because a lot of the visitors are Croatian.