The biggest problem with these is that the writers of the OC Donut Steele get an anurysim if you don't like their character, and they might fight tooth and nail against that, forgetting that this is the game and thus, should serve the player.
I don't know if any of the writers get upset about poor receptions, and frankly, it doesn't matter. I don't think that the fact that this is a game means that things should be changed for specific players. Games have audiences that they're intended for. There are things which devs/writers may be flexible on, allowing for variance based on the wants of certain players. As Alypia said, though, aside from certain variance for some characters, all the options you really need are "I don't particularly want to fuck you." Of course some characters are going to show up and be more persistent than others. Ryn is important for the plot, but now that a dildo has been added to allow Ryn to fight without being handicapped if you aren't fucking her, you can pretty much just avoid all sexual interactions with her. She was pretty much all the only character where it ever seems you need to fuck them, and even then only because she's mandatory for the Winter City/Ice Palace. Unless you're defeated in a fight, you can pretty much just say no to any and all sex if you want. That is how you're served.
Aside from that - flesh out existing character more before making new ones, more transformation options for NPCs.
That cursed paladin lady that's been in the game forever comes to mind. About time she gets a quest to fix her (revert to female, return her vag and make her futa or do nothing) and becomes a comapnion.
And what's even with that elf "princess"?
1: Yeah, it's probably better to make characters more fleshed out, but while transformation options are nice, every transformation adds a new variable, so either characters need to be written with future transformations in mind, or scenes must be generic enough that a character fits in, regardless of body parts. This also presents an issue of someone were to go with your suggestion of options that make wide, sweeping changes, like "all furries are not furry" or things like that. That means a lot of extra work to rewrite characters, perhaps even into ways that simply don't make sense for who they are. That, or turning all of their scenes into generic mush. Also the time and money to commission alternate artwork to represent their changed state. To make the changes satisfying, a lot of work must be done, and that work, these new features, may still simply not suit the character.
2: Eryka. That's the paladin. Of course, it would be neat to get to do something to help fix the corruption, but she's not going to be a companion. Companions need the most work out of any character in the game, because they follow you around. So of course, they need the ability to comment on things. Eryka was never intended to be a companion, so she'd need a ton of dialogue to be written up to insert herself into the companion circle. Hell, Shar was originally supposed to be a companion, but that idea was abandoned because of the workload. If an existing character were to end up becoming a companion now, I'd expect it to be Shar because she was intended to be one, but even so I'm certain it won't be done.
3: As Wint3r said. Why did you put that in quotes?