I'll second opinions on inner conflicts, it not only makes the protagonist more relatable & human, but it reflects on the writer's self-awareness as well, it's an effective way of communicating "I know that this is messed up by real-life standards" while still allowing a given fantasy to be played out.
Related to that, I'd like to see more corruption games that includes a male protagonist as one of the corruptee - or males getting corrupted period. We've got plenty of men MC corrupting women, plenty of women MC being corrupted, but I feel corrupted dude is an under-exploited niche.
Generally speaking, I'm a sucker for displays of affection, even in games that have less of a romantic focus. Us humans do a lot of non-verbal communication, which is unfortunately tricky to do in a visual medium that doesn't include actual human actors - you can't just tell your 3D model or drawing "make that face", "caress her face", "hold hands", etc., you need to explicitly model it.
Another thing I'd like to see more in games that include some kind of branching is better feedback regarding the effects of player actions, like "you are seeing this because you replied that in an earlier conversation". There's already a fair number of games that do this, either through ingame walkthroughs, unlockable galleries with clues & other types of feedback, but I still feels this an underestimated time investment. Basically, if you don't give player feedback, they may not realize how complex your game actually is & will therefore underestimate its replay value.