Buses are faster, more reliable and more frequent (there are only 2 trains a day on the Ploce-Mostar-Sarajevo route - one of which is too early if you are coming from elsewhere).
From Ploce to Mostar and Mostar to sarajevo, the bus and train run through the same valleys, and are always crossing each other so scenery is roughly equal. Though i haven't done it for a few years, train was cheaper when i did (even cheaper getting a bus Dubrovnik-Ploce, then training it) though for through journeys with the change in Ploce takes a bit longer
From Split/Dubrovnik there are through buses to Mostar and Sarajevo (and there are also tourist coaches for day trips), or you can change in Ploce (which i did last trip) onto a bus or train. Ploce has a strange status, but is a fairly drab place so there's no reason to really hang around (though if you have a day, you can get a ferry out to some islands).
And if you do get the train from Ploce, be aware that the ticket office (and station in general) is often entirely deserted unil30mins or so before departure, so don't panic that you haven't got a ticket an hour or so beforehand
In croatia in general, buses and boats are much better than trains. I would only realistically suggest using a train if on the main East-West corridor (Slovenia - Zagreb - Vinkovki - Serbia) or if going through to Vienna or Budapest (still very slow). Along the cost etc, you are almost always better using other forms.