Ohhh to continue on with that "where in Touhou do you feel it could be a stopping point/ending for the series", I feel like LoLK really gave us everything for a finale. I feel like a lot of the series has built up the Lunarians as a big bad villain and you finally got a chance to confront a few forces on it in the game. If it maybe focused more entirely on Lunarians instead of Junko's revenge then I think that would be a good place for it to end
The Lunarians have definitely been built up as powerful antagonists, but I definitely wouldn’t say they’re the major villain of the series. If anything, their purpose is to be an absolutely unbeatable force that puts the problems of Gensokyo into perspective. Even in LoLK, you fail to so much as put a scratch on Sagume.
Don’t take this analogy too literally, but it’s somewhat like telling a story about a small kingdom neighbored by a larger empire. You can still tell an entirely self-contained story about just that kingdom, it’s succession problems and whatnot, without ever toppling the empire. In fact, it would make no sense for the kingdom to topple the empire. Even if they’re a constant threat through the story, the villain is always going to be the Evil Vizier who tried to assassinate the Princess, not the Empire. That doesn’t mean the empire is irrelevant or even unimportant to the story, they’re just not what it’s about.
Touhou is about Gensokyo, not the moon. It’s not even about Gensokyo being invaded by the moon. The moon is just one of many concerns to the people in Gensokyo. If there has to be a final story arc to the series as a whole, I would imagine it would come from WaHH, specifically the subplot about the sages and therefore the creation and future of Gensokyo. That’s much more relevant to the unifying themes of the series than the moon is.
The big bad villain is Kasen.