Bus versus train

In this case I'd take the 8:25 am Flixbus.com direct which is only 4 hours and faster and better connected than any train.
It is currently listed for $20. I've been on Flixbus before a couple of times and it was clean, the thing is you want to go to the toilet before you get on since there is only one on board. Just download a couple of good movies and the trip will be over before you know it.

There is a train that goes direct but it takes 6 hours and does not get you to Zagreb until almost 10pm.

In the past we’ve taken the bus. I don’t remember it being an awful trip.

Four hours on a bus or six hours on a train? Does it matter? It sounds tedious either way. I guess I vote for the train as it's a bit less claustrophobic.

If this isn't set in stone yet, and if the intent is a visit to more of Croatia, then consider doing Croatia in the opposite direction and starting in Podgorica. The flight is non-stop in about 75 minutes and depending on how you pack under $50. But you will have to leave on 1 October.

I have taken the train from Budapest to Pecs, Hungary, which is in the southern part of the country. I'm not sure if trains from Budapest go on the same track to Pecs and Zagreb.

My comments are mostly general. It was pleasant, 3-hour trip from Budapest to Pecs. I have mostly taken trains in Europe.

However, I have taken buses a couple times in Europe for long-distance trips -- principally in Ireland as well as Portugal and Spain. In general, I like the relaxed pace as well as the better views of a bus when I have the time for them.

In general, Flixbus is clean and pretty dependable. There is a restroom on the
bus but there are also breaks every couple of hours to get out and stretch, get
coffee/snacks, and use a "real" WC. The wi-fi on the bus is the only thing I'd
say can be a bit spotty.

Flixbus is the way to go--4.5 to 5 hours.