I know you can skip the trans content because I did. (Just not my thing) The femdom content seems to be pretty light. Obeying the captain's orders. It seemed to be more playful/roleplay femdom on her part because she actually seems to be really cool and friendly otherwise so, not sure I'd actually call it femdom at this point in the game. I really like the relationship dynamic of the crew members so far.
The only way to stay friends is not visiting them.
What would these choices have been about exactly and where would they have happened, if it's okay to ask?
Just things like mentioned before, being platonic instead of romantic in the sub stories.
You gave choice for everything so i'm curious why there was no REAL choice for the forced hj by piper. Rape tag will lose you potential players and also those who don't like forced femdom. The scene has little to no impact on the game and story and doesn't really merit the rape tag.
I think it does have an impact, as it's intentionally there to set a tone and people have certainly mentioned it many times. We're also never going to please everyone so that part I'm fine with.
From what the dev was saying, the sister is going to have her own story going on separate from the crew with her own LI's.
I'm unsure yet, haven't given details only the general layout. I'm going to assume multi protag but main focus being on the male MC.
OK so if I'm not sexually interested in a character, I don't visit them even if I lose a tad of info on their background (and MC's)
It's all part of my elaborate denial fetish scheme.
*GASP* Your kink is kink-denial! You MONSTER!
.More of her pls 
