This is what I would have done.

Everyone starts off with the ability to purchase an apartment.

As you continue through the game and your reputation spreads through your deeds (i.e. completing ARR for example), you would be able to buy a small plot of land in one of the three major city-states.

When you complete the MSQ of heavensward, you'd unlock the ability to relocate (if desired) to:
1) Ishgard
2) Sharlayan
3) The sea of clouds

You would also unlock their architectural styles for your home

Upon completing the MSQ of Stormblood, your heroics would earn you the option to relocate to
1) Shirogane
2) The Azim Steppe

As before, you'd unlock their architecture for your home.

Now, so that this wouldn't be a race to see who could complete the MSQ the fastest, the actual housing wards themselves would be separated into
a) Instanced FC wards and
b) Instanced personal wards

This way, as you grow as a character, so too do your options for owning land. Everything, including mog station purchases, goes with you when you when you move, through the miracle that is pack chocobos.