Please, don't pay too much attention about the complaints. In this part of the world complaints are a kind a "national sport", but the praises are always withheld because a good service is something that goes without saying. Frankly speaking, I am using the services of different bus companies on daily bases within my town and its surroundings and on weekly basis for travels between my town and other Croatian towns. Honestly, it is so hard to put them in some realistic order regarding their quality of service, but I can tell you, they are all fair. Probably Autotrans, that you have asked for is among the best, but Croatia bus has wider network and far more buses. Well, with such a wide network and a huge bus fleet it is quite normal that something can happen. It happens all over the world, but its service is in general, fair.
You can choose between Croatia bus and Autotrans, but also among other bus companies that ply on Dubrovnik to Split route and you will be satisfied. I can guarantee this with my own, two decade long, intensive experience using their services.
Online booking on Croatian bus companies usually get you an assigned seat, but there are instances where this practice is not the case. Those instances are, for example, short regional lines (under 100 km of distance) and the long distance lines during the winter or let's say off season period when the buses are never filled to the last place. During the summer time and using the online booking, especially on the route between Dubrovnik and Split and some other high frequency lines, you will be definitely assigned with a seat i.e. your seat will wait for you.
One more information. Even when you book your ticket online and have an assigned seat, most companies (although not all of them) are charging the luggage per piece upon your bus boarding. So, when you arrive at the bus station, you will have to pay to the conductor for every larger piece of luggage a price of roughly 10 HRK paid in cash (roughly 1.3 EUR or 1.4 USD). Cabin luggage is free of charge, but it can be only of small dimensions.
In any case, whatever your decision will be, just book your ticket in advance for your peace of mind and don't worry about anything, but just sit comfortably and enjoy the scenery.
Hope this helps.