Subs are lower profile units by their very nature. Capital cities tend to make more sense with significant surface units. Of course the US names its subs after its cities. However, with the attack naming system you have quite a good format for 12 subs and suitable names.
Melbourne being used on an amphib isn't impossible. Choules will need to be replaced at some point. There is evidence the government is considering a AOR/LPD type ship in the near future.
We are at the point where the RAN could consider a 3rd LHD now the first 2 are a proven quantity and FOC. In addition land400 and other loose ends are much better known now. Other higher risk projects are also underway and competed. The future frigates look to be very capable.
Bringing in a 3rd of an existing type is entirely possible. Doesn't mean its likely. IMO I wouldn't be surprised if the name is rested and earmarked for a large surface/sea-lift/amphibious/aviation ship. I am skeptical of it being used for F-35B's. More likely as an amphibious ship, perhaps specifically supporting Land 4503 (Tiger replacement), ASW (with some additional MH60-R), Chinooks (lift?).
Biggest issues against it are crewing and local construction content.