Following is a ranked list of my favorite female protagonist games. My list is based on my personal tastes so not saying these are the best games or even good for other people except me. My tastes being, dark themes like blackmail, corruption, prostitution, bdsm, and drugs among others. The more a game immerses me into actually being the protagonist the better. And the most important factor: how much the game actually turned me on.
1. Good Girl Gone Bad - has the best of everything and can recommend this to anyone (except maybe the 2d art is not to everyones liking, but i love it). Has many choices, good story, and frequent updates. Is among the top 50 patreon supported games so hopefully this makes for updates to continue for a long time.
2. Katies Corruption - a much hated and loved game that checked all my kinks. Main complaints are that not enough updates and character is a retard. If you play this game for the first time the amount of content is big enough for hours of gameplay, the reason for complaint is that updates (biweekly or monthly) are just one scene or two now. And regarding retard comment, its the player making the decisions, sometimes acting retarded is a subconscious response for wanting a good rough punishment (again a personal kink).
3. Annas Exciting Affection (Renpy Mod) - has better models than previous 2, but listed after because the corruption of protagonist is still not as advanced. Suffers of same retard criticism, but again, i think that in real life no one always chooses whats best for them and we let our bodies and emotions get the best of us. In all these samey games are my preference, I assume the protagonist acts "retarded" because she has some serious repressed submissive sexual fantasies of being dominated and abused.
4. Lilly of the Valley - could be ranked higher but its in RPGM and having to play the walking around part in chubby japanime sprite art frustrates me and breaks immersion. Past that, has one of the best models, art and animation. The corruption process builds slowly which makes for a better immersive experience.
5. Fashion Business: Monica's Adventure - this game..wow... this could possibly be my number one game except it just started out. The art is the best anywhere and the story is developing at a slow but immersive pace. The amount of hate and love for this game in its thread is even worse than Katies Corruption, and rightly deserved of both. The game is just at an early stage so of course it has some frustrating mechanics and not much sex content yet. And it has the dreaded RPGM engine. However, the game creator is listening to all feedback and making changes to the most frustrating parts, he is amazing.
6. California Bound - this one really immersed me into the character the most of all games listed here. Unfortunately the game creator has the project on hold, he mentioned to continue updating it on May. He also working on a rework to make the story more slow paced. If he fulfills those promises, this game has the potential to be my favorite.
7. Angelica's Temptation - newish game that has enough content to have provided me with a very satisfying experience. Very heavy interracial NTR (at least i went those paths) with good Cg models and animation.
8. Sensual Samantha - bullied and abused by lesbians, weird this turned me on despite not liking lesbian content in games. Yep, a good one with a character that at times looks ugly or beautiful, but we all have bad hair days too.
9. Eleanor 2 - Lesson of Passion game with excellent art and animations. Little older and grindy by today's standards or maybe not. Could satisfy more players as you can go full romance (zzz) or whore (yes!).
10. Green Shadow Rachel - female superheroine gets corrupted is my favorite theme ever. This little gem will forever be in my heart. The Jessica Jones of porn games.
Ok had many more but want to stop at 10 cause sounds cooler as a Top 10 list.
Better female protagonists games have been mentioned in the posts above. Of which the best ones are Coceter Chronicles and Zoes Temptation. Unfortunately, despite they being well made games artistically and story wise, they didnt satisfy my kinks.