I used to live in WA but visit once or twice a year now as my kids still live there, so know it well from a tourist perspective as well as past resident.
I get what you mean about relaxing on Rottnest, but options to do anything other than swim/sunbathe/snorkel are few and far between. I'd chill in Fremantle as you are still close to South Beach (especially if you look in the Thomas Street area for a self catering cottage) and all the lovely cafes. shops and galleries and the market, that Fremantle is famous for. If it's hot, you get the afternoon sea breeze, aka, the Fremantle Doctor providing relief. It has a lovely relaxed vibe and much nicer than Perth city. From Freo you can get the ferry to Rottnest, either a day trip or overnight - it is with going to, if only for the Quokkas! Snorkelling is good too.
Free is a good base for getting to Perth city if you want to, by ferry or train, but also good for heading south to the Karri forests, wineries and Esperance (8 hour drive). As I said, the area there is stunning (water is not very warm, but warmer than our sea in summer).
The orca trip we went on in February from Bremer Bay was wonderful and we got really close to several pods - there are occasion blue and sperm whale sightings from the boat too (Naturaliste Charters).
The coast from there, to Denmark is also beautiful, and Denmark is a nice base for a day or two, then Margaret River for the coast and wineries - three hour drive back to Perth from there.
Hope this helps!
We'll be back in December/January - doing a house swop in Freo...
