So, here's one story idea i had, keep in mind that there's more where this came from.
So, the story is about this guy in a typical harem situation in his high school with his osananajimi and tsundere heroine etc etc. Turns out that he himself is originally a spy sent on a mission to infiltrate another country in a war between them. He fails and is kidnapped and lost his memory. Thus, he is placed into a VR simulator where he is made to believe he is living the life of an ordinary student with his harem of girls, who are actually the virtual counterparts of female agents specializing in information extraction, hoping to use the simulator as a proxy to pull out his repressed memories of his homeland to win the war for their country.
Themes: this world is not real, everybody who means him no harm is virtual, and everybody who is real is is enemy. Possibly having earlier branch endings where the hero settles down with a girl without ever knowing the secret behind the world, *also implied that doing so lets the girl access the secrets she desires*, with the true ending being him discovering the secret behind the world, the girls going all yandere and changing tack to killing him again and again in VR, stuff like that, and him possibly breaking out of the facility... or not. (can have a All Ends Are Bad scenario where he gets killed after he wakes up if you are dissatisfied with a happy end for him) :X
maybe this is too difficult / ambitious for our first try at a vn?
Developing it further, I thought on of the core themes of the story can be to "remain true to yourself even in a world of lies". In that sense I want the protag to actually not be an asshole (like all harem protags tend to be). Since the world is a virtual one all of the heroines are actually more like players in a game. As such the persona they exhibit to him (genki, kuudere, tsundere etc) can actually be false, like more of the person they wished they were rather than who they actually are in real life. That can be a plausible reason for them eventually being (truly) attracted to him as well, because his own emotions are the only one that are true and they recognize their inferiority in this aspect. Like the tsundere can actually be an angry emo kid, the meganekko kuudere is actually a genki irl, the genki girl is actually a shy, quiet girl. All of them would be 'pretending heroines'