There are no direct flights between Kuala Lumpur and Brisbane after the only operator, Malaysia Airlines decided to ditch it in August 2015. There are still no direct flights between KUL and BNE today, however, you will soon have one additional choice to choose from beside Qantas or Thai.
Malindo Air, is a joint-venture between Malaysia and Indonesia (thus the name) and contrary to what is written on Wikipedia, it is not a budget airline albeit being owned by low-cost carrier Lion Air. Bags and meals are included in Malindo’s ticket price. It is a full-service airline.
Malindo Air is expected to start their inaugural flight from Kuala Lumpur into Brisbane via Denpasar on the 31 March 2017.
A quick search on Skyscanner will show that you have a few choices to choose from, specifically on the sector between KUL and DPS. Depending on dates, there are at least two to four flights a day between KUL and DPS. So pick your flights carefully in order to avoid waiting too long in Bali.
Anyhow, the prices ain’t that great of a difference considering that Qantas is about a couple of hundreds dollar more. Yet, if visiting Bali and then Kuala Lumpur is your kind of holiday, then Malindo might be what you are looking at. Again, if you are travelling with a big family, the savings can be significant.