On MEL-SYD I can't see it making much of a difference, but perhaps for intermediate towns. Flixbus or not, I think for many people bus is a distant 3rd behind planes and trains.
The timetables are not published in a convenient format, but can be worked out through laboriously making individual queries for each stop.
FlixBus hardly serves any intermediate cities on MEL-SYD-MEL. The only options are to travel MEL-ABX or MEL-CBR in addition to the various SYD airport and CBD stops. (And obviously ABX-CBR etc.)
The V/Line single rail fare for Melbourne to Albury is a bargain $11.00 on weekdays, lower on weekends. Seniors pay half that, and free on weekends. The standard gauge VLocity railcars have a buffet (although if it's two sets coupled together, one may be closed).
The NSW TrainLink XPT is far more comfortable (even in economy seats, but better in first class seats and best if you can snare one of the 18 sleeping car berths) than a road coach between MEL and SYD, and at least 50 minutes faster than FlixBus despite the circuitous steam-era tracks between Junee and Goulburn, NSW.
The XPT has coach connections at a choice of Yass Junction (closer to CBR and my preference) or Cooramundra to and from Canberra.
There are only three XPlorer railcars each way daily between Canberra and Sydney, but while slower than the coaches (assuming the latter don't get held up in traffic), they are again more comfortable with an on-board buffet adding to the attraction.
FlixBus also lacks suburban pick-up or set down stops in Sydney and Melbourne: the trains for instance stop at Campbelltown and in Victoria at Broadmeadows, as well as Seymour, Benalla and Wangaratta, plus the XPT serves Wagga Wagga and Goulburn in NSW as well as the NSW Southern Highlands' Moss Vale (with Canberra trains also stopping by request at Bundanoon, Bowral and Mittagong).