A good question.
A local answer.

Fremantle can suit a market morning; a Perth base can be easier if your arrival and other plans are city-centred.

Consider an easier first stop and divide the south-west route into manageable daily drives.

Compare the train's convenience with the river experience you want; the cheapest way to reach Fremantle may not be by boat.

For Rottnest or a regional tour, book the departure first and then plan the connection from your hotel.

Check rental desk opening and any after-hours fee before assuming collection on arrival is easy.

Buy only what your kitchen can handle and leave room for a bakery or café discovery rather than prebooking every meal.

If you will cook, choose a seller near your accommodation so seafood stays cold on the way back. Rottnest is better treated as an outing than a grocery stop.

Choose a small number of wineries, beaches and walks by your shared interests. Leave an unplanned afternoon for a relaxed meal.

Reserve island tickets and accommodation first, and leave the Margaret River attractions for a separate day.

Choose Perth if city sights and airport access matter most; choose Fremantle if the waterfront and its local streets are the main attraction.

Compare a train-based route with a direct ride using your terminal, luggage and final Rockingham address.

Do not try to combine two distant outings in one day. Compare departure times and daylight before booking.