A good question.
A local answer.

If you go into town, choose one area for dinner and a walk, then book or plan the return transport in advance. Check the current late-night service rather than counting on an old timetable.

Check your actual arrival terminal and the airport rail station connection on the official map. Terminal location matters more than the airline name.

Choose the season and experiences first: southern towns, forests and coast make a different trip from the long northern route. Three weeks can support depth in one region or a carefully planned split.

Confirm disembarkation and airport check-in times, then choose whether to spend the day mostly in Fremantle or split it with Perth. Both can be reached without a rental car, but transfers consume time.

Check luggage storage on the transfer day and airport travel from the final base. Seven nights give room for a split, but it should improve the trip rather than just follow an arbitrary ratio.

Pick one or two southern bases with activities the children can enjoy nearby. Several short stays may cost more energy than the scenery is worth, especially with a toddler.

Choose one base for all three nights unless you have a strong reason to move. Packing and checkout time can outweigh the benefit of a single night in each place.

Map your likely evenings and parking costs. The CBD shortens access to central sights, while a Subiaco stay can work well if you value neighbourhood dining and the parking arrangement is real.

Cluster Whiteman Park and Swan Valley if the route works, but check which attractions actually operate in winter. Book the vehicle and child seats ahead for holiday dates.

Check ferry, bike hire and weather details before committing to Rottnest. A windy or wet day can make a short local walk more rewarding than an expensive island outing.

Keep the trip flexible if the crossing is the deciding factor. An enjoyable Perth or Fremantle day is a sensible backup when conditions are poor.

Choose one direction beyond Perth. Those destinations lie on very different routes, and trying to connect them all would turn five days into a driving exercise.