Traveling by bus Prague to Vienna and Vienna to Zagreb

I've taken Flixbus once Munich to Salzburg and was impressed by the service that comes with the low price in comparison to Greyhound and Eurolines (the other European based long haul bus company).

However I don't like rides that last more than 3 hours anymore.

I would just take a train from Prague to Vienna. The whole route is through a river delta. And not particularly scenic.
From Vienna to Zagreb, Austrian and Croatian airlines would be preferable and save you time. The Alps are south of Vienna and they make travel a little difficult on the ground.

From Prague to Vienna, no reason to go by bus; there are several direct, very inexpensive trains per day. See them on the Czech train web site cd.cz. Enjoy your trip.

I took Flixbus from Krakow to Budapest last September. The bus was quite basic, not what you'd call tourist class, but maybe from Prague to Vienna they have better vehicles. The bus was nearly half an hour late leaving Krakow, presumably because of traffic getting through Krakow (from Warsaw) to the station, then another delay of almost half an hour because of some rowdy passengers, then because of the late arrival into Budapest long delays because of rush hour traffic.