A good question.
A local answer.

Check the grade and transport for any Bibbulmun Track section before treating it as a quick city walk.

Choose accommodation near a useful station or bus link, with groceries and evening meals within a comfortable walk.

Keep a city or Fremantle day as a break from beach weather, and follow current surf and heat advice.

Plan the full journey to the ferry departure point with the current transit planner before purchasing island tickets.

Set overnight towns from comfortable driving days and the child's break schedule, not the farthest place on a map.

Keep the final night near the departure point if the return drive would otherwise threaten the flight.

Choose short walks and markets that work for the whole group, then offer an optional longer activity for the teens.

Give one day to the city and river area, then choose either Fremantle, a beach or a wildlife outing for the second.

Tell the hotel about the late check-in and confirm a fallback pickup if the last public service is missed.

Leave a flexible day for weather; beach, river and regional outings do not all need a fixed date.

Compare the specific hotel's walk to dining and the beach rather than assuming the whole suburb is equally convenient.

Check today's group-ticket rules and child fares; a price quoted in a much older forum thread is not reliable.