I suppose for locations like the Blue Mountains, it can depend on just what you want to do whether you spend two or three nights, like in your two days/nights you could cover most of the major lookouts, scenic cable car etc. but if you are pretty fit and active, there are some good walking trails throughout the area, out of the way valley locations for accommodation that could be more rewarding re wildlife and the http://www.jenolancaves.org.au/ , a place you might want to spend one of your nights at if that is of interest to you.
Melbourne is worth far more nights than Geelong and in fact I would only stop to get the vehicle or maybe not even get it there - I'd check if you can take your hire vehicle on the Sorrento to Queenscliff Ferry and then get one in Melbourne, there being some hire companies that have depots out in the south eastern suburbs ( so less hastles with traffic ) - http://www.rentabomb.com.au/?laststatus=pc&mrtype=pc&postback474=1 ( don't let the name fool you for they started off catering to cheap hires but nowadays and having been around a while have a full range including new vehicles ) and a location like Blackburn or Dandenong could suit you as follows:
. Day 1 hire( from Blackburn) - head for Healesville Sanctuary and lunch, an afternoon devonshire tea in The Dandenongs and then on to Phillip Island for Koalas, check into Accommodation and off to the Fairy Penguin Parade.
. Day2. head around on to the Mornington Peninsula ( wineries/walks - Point Nepean where you can near touch the ships as they go through the Rip ) Lunch or Dinner at the Iconic Portsea Hotel - out the back facing the bay and either stay at Portsea, Sorrento or get a ferry across to Queenscliff for dinner and accommodation there.
. Day3. You are off and onto the Great Ocean Road via Ocean Grove/Barwon Heads ( you've missed all the Geelong traffic area )
I'd stay just the one night at Lorne and keep the two for Yuulong as it will allow you to have a couple of evening/morning Apostles vistas - sunset and sunrise or alternately just the one there as planned and then on to Port Fairy - are you going to be there for https://www.portfairyfolkfestival.com/ - if so, great and better still if you have got accommodation and if not, you are missing a great gig.
Anyway, with one night at each of Lorne to Port Fairy, you might have a day up your sleeve for either an extra one in Melbourne or two at Halls Gap.
Have a look at http://parkweb.vic.gov.au/ for some great ideas close in and further out, http://www.studleyparkboathouse.com.au/boat-hire-make-your-special-day-one-to-be-remembered/ a great place for lunch and a row on the Yarra.
Have you also considered the possibility of rather than two days at Ballarat ( there is some interesting stuff there like Eureka Stockade /Blood on the Southern Cross show/even night there ), you keep heading west to Adelaide and catch your flight to Perth from there.