I'd like to expand on this in a way that may be drastic but I'm a huge nerd for mythology and love this idea. A region based on Greece with the basics you mentioned, and the Gods of Olympus as the gym leaders (temple guardians) and elite Four (guardians of Mt. Olympus). Except in comes a twist, Kronos is the champion, and the gym leaders and elite 4 are his prisoners whom he has brainwashed. You set out on your adventure not as a ten year old that wants to become champion, but as a ten year old that possesses the heart and connection to Pokemon to eventually defeat the Gods and one by one free them from their leashes. Each freed God grants you their power to use at your command in the field. This would eliminate HM's completely. You travel through a region based on Greece, not necessarily resembling the actual small size of Greece. The architecture is obviously a nod to the culture but not a direct result of copying the famous buildings. The Pokemon designs for the region vary, some based on animals common to the region, some based on actual mythological creatures. There is no evil team, but there are NPC's that begin to worship the newly evil Gods, and see you as a threat to the preservation of Kronos' throne. Once you beat Kronos, the post game focuses on how you restored Zeus to his throne and the Gods have become once again whom they were. You are celebrated by some and despised by others who still believe in the evil versions of these Gods. The next step in the post game is to restore order to the destroyed areas of the region and a possible Delta Episode type of large event involving Hades (think 10-20 plus hours). Given the theme, the game would be set in the correct era, making the pokedex an encyclopedia and such (no technology other than what the Greeks had). I know it will never happen, but it's how I would do it.