Kingdom of Deception - Main character was betrayed by her family, sent into a trap laid by orcs and captured, she is then forced to try to climb her way through the orc camp's ranks, proving her usefulness to them in order to eventually claim her revenge.
Good Girl Gone Bad - While this game is one I haven't touched in a while, that's not to say it isn't worth playing, I plan to play it again when it gets finished, it just hasn't been done yet. Also female protagonist. You play as a girl at a crossroads, her family is falling apart, her scholarship is being defunded, and she's got choices to make that will shape who she becomes.
Offcuts - Technically this game is 3D, but it's run through a filter or painted over in a way that makes it look more like 2D. You shouldn't run into the uncanny valley stuff you might be worried about with 3D. More to the point, however, it's a high school romance game done pretty well. I enjoyed the story, felt a connection between the male MC and the platonic male friendship he garnered with another character, and just, overall, liked the girls and enjoyed myself.