I believe that the reason the mainline domestic aircraft do not use flight numbers as their callsign is because there is potential for two aircraft with the same flight number to be airborne at the same time which would obviously cause ATC problems. eg QF515 BNE-SYD-PER, if the BNE-SYD flight is delayed it could be inbound to SYD at the same time the SYD-PER flight departs SYD.
I think that aircraft rego's will continue to be used for mainline domestic ops. GB