Travelling to Australia - should I combine Melbourne and Perth (September)?

I'm travelling to Melbourne for work. This is my second trip, and I did cover the basic tourist attractions during my first trip (including Great Ocean Road and Yarra Valley). I have a couple of days free in Melbourne and was thinking of going to Mornington or Phillip Island for the penguins. I also covered Sydney and Cairns during my last trip.

I have around 5 days after work and was thinking of travelling to Perth. Firstly, is this a good idea considering the distance, and if not, any alternate suggestions? I really wanted to go to Whitsundays but it generally seemed too expensive this time of the year.

For a quick trip, this is what I thought of covering in Perth: Perth city, Pinnacle Desert (with stargazing), Rottnest (should I stay on the island overnight?), Fremantle city, whale watching from Hillarys Boat Harbour. Any suggestions?