Alright I guess I've ran out of excuses not to play it, I'm almost done with Lovesick Puppies and still have a bit of time before the July releases so might as well start this one.
Harem game, not nukige, emphasis on story... tough criteria there, considering harem isn't my forte. I guess you could count all the Eushully tactics/RPG games, they're definitely harem though some do have character routes like Arterial or Alchemy Meister. In the same vein, you have most of the
SoftHouseChara games fall in the same category. As for purely story VN,
なないろリンカネーション is very good and features a harem of demons. The "sequel"
あけいろ怪奇譚 is even better but there's only a single route with multiple (loli) characters at the same time.
ノラと皇女と野良猫ハート has one route where the protagonist ends in a harem with three sisters, very good game
IF you can stomach Hato's style.
EDIT: I forgot the Baseson's Koihime series, I haven't played them personally but they're generally highly recommended by people whose opinion I trust.