It will be a difficult task, but I would move it towards the Hellenics colonising various other areas, from Home Cities such as Athens on Thebes.
Areas would include Sicily, Southern Italy, and perhaps even Asia Minor.
Another idea would be instead of calling the cities 'Home Cities', they are instead cities you ally with.
So you are a small Greek settlement somewhere, and you're allied with Athens. It would work the same way, except you could perhaps 'ally' with non-Hellenic cities.
I'm also tentatively under the belief you could mod AOE3 so the access to the Home City is removed, and that feature is destroyed all together.
It may be unlikely, because of the way the Home City is integrated so entirely into the pre-game and post-game and main-menu, etc, rather than solely existing within an individual 'skirmish'.
Maybe you could remove the city graphics, and make it a simple 'screen', with buttons and stuff (which are basically cards and decks).
This means you don't have to even use the City concept, Home or allied or otherwise, as you could receive the 'shipments' through any means.
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