Yes, I always forget the Uncharted Waters part of the title for some reason. It really is one of the best games I've ever played on any system. I really don't even think of it as being in the simulation genre. It's much more of an RPG, at least in my mind. If you've ever played Mount & Blade, I think the dynamics are somewhat similar. Also, Sid Meier's Pirates was an attempt at a very similar PC update, but in my opinion it was not nearly as good.
I know the series by its Chinese name, which is written the same as the Japanese name in kanji, 大航海時代. It means the great age of sailing / sea voyage.
You are right that this genre isn't really a simulation game. I wouldn't call it an RPG either, even though you choose a character in the beginning, but you're managing your fleet with an overlord UI. I would categorize it as a turn based strategy game. I actually have played quite a few turn based strategy games, most notably the Romance of the Three Kingdoms series and the Civilizations series.
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Your gameplay style sort of dictates whether it feels more like a turn-based strategy or RPG with turn based combat. I always played avoiding combat as much as possible and focusing on exploration and trade, so it felt more like an RPG.
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You are right again. I kept thinking when in map / management mode, it's also turn based, but I was wrong. Only the combat was turn based. Playing in the map and entering towns/cities were all real time.
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