Aegean Sea. Legendaries would be a turkey/archer thing for the Ottomans (flying steel?) while the Byzzies would be represented by a massive two-headed Eagle/wall thing (flying/rock?).
You would start in Morea, with Gym towns in Mycenae, Athens, Thessalonica, Halicarnassus (Bodrum), Syrmna (Izmir)/Ephesus, Ithaca, Adrianople, and Nicaea.
Futher towns located at:
Sparta, where obvious tutorial journey city is obvious.
Delos is a dark joke here by making it a market town with a department store that lets you buy Pokémon as a sly reference to the Roman practice of using it as the main hub for buying an selling slaves.
Legendary-related ruins at Troy, Mt. Athos, and in Crete-analogue.
Mykonos exists as a resort island not unlike Undella in Gen V.
Evil Team base is located in Thermopylae or Myriokephalon (maybe version-based?).
Large port city like Slateport in Gen III modeled off of Dyrrachium (Durrës).
Pokémon league and Victory Road will be modeled off of Constantinople/Victory Road. Galata/Asian side of the straits will be V. Road, while the Hagia Sophia or the Blue Mosque depending on Version will be the actual Pokémon League. Champion, despite it being edgy, will have a Thundurus.
Post Game area if it exists will be either Cyprus and the coast of Syria or Sicily and southern Italy. If the former, we get a second evil team based off of Isis, and if the latter, we get Team Rocket back.
Starters based on a Nemean Lion (Grass/Steel), Pegasus (Water/Flying), and Lernean Hydra (Fire/Poison).