The female protagonist tag is a good place to look. There are also a lot of games written with a "blank" protagonist whose gender is never specified, or with a gender choice at the beginning that never impacts the plot.
Looking for games to recommend to you has really impressed on me how few non-male games there are on this site. Jeez.
Detective 1: Blacksea island- This game has a female protagonist. It's a mystery game where you wander around finding clues and eventually solve a murder. This is more game than story, so I'm not sure it's what you're looking for.
Price of Freedom- Select your gender at the start of the game. Survive as an adolescent gladiator in ancient rome. I don't recall any sexism, and there are several strong and well-developed female characters. That said... it's ancient rome, so there may well be some I'm forgetting.
Diplomat- This one is by me, and features a gender-neutral protagonist. You're a diplomat deciding how to handle communication with alien races, both in first-contact situations and ongoing relations. Long-ish, with several different storylines.
Secrets of the Crag- Also by me, with a gender neutral protagonist. You explore a cave system full of treasure and monsters. Long-ish, but not narrative-based, so I'm not sure it's what you're looking for.
I also strongly recommend Mystic's games, linked above. They probably fit your length criteria best, and are very well written.