My visit to Australia was Oct-Nov 1998 and, while I did not visit the Great Barrier Reef plus I stayed with friends in Sydney, I can recommend the following:

Melbourne - Saville Park Suites Melbourne (although I believe it was part of the Holiday Inn Suites group at the time) on Exhibition Street in the CBD. My suite was a beautiful, large, one-bedroom apartment, MUCH larger than my own in Chicago, with complete kitchen and dining area plus full-size, private washer and dryer. I liked the quiet and convenient location too.
http://www.savillesuites.com.au/melbourne.html

Adelaide - As above, the all-suite hotel where I stayed was part of the Holiday Inn Suites group of properties but, now, it is the Saville Park Suites Adelaide in the West End on Hindley Street. I had a studio, which was much larger than any studio apartment I've seen for rent, including kitchen and private laundry facilities.
http://www.savillesuites.com.au/adelaide.html#

At the time, the rates for both locations were very competitive and no more expensive than most standard hotels in the area. I booked the accommodations with a travel agent when I was staying with friends in Brisbane; don't know if that made a difference in the rates I was offered. Hope this helps - have a wonderful trip!

Bill