Both the love route and the slave route are not equal. As the options you choose should make clear, the love route is for story, the slave route is for sex.
Yes, that slave training contest is planned to be remade into something else at some point, it doesn't totally fit with the flow of that arc.
The elfbots use elf blood as the energy source, I'm certainly not trying to present the concept as good. That's Trenero's job. If people only hear the good things, the project will get greenlit. Only a very few elite people, and you and his daughter, know the dark secrets of how the elfbot is made at the moment.
Lin started out as a hopeless slave who now has a former royal and Nia following her. I won't go on, like you say, you can see the glimmers already.
Kali has went from a lazy girl with no accomplishments to a somewhat ambitious one at the moment, she's beginning to strive for great things and her level of skill has improved vastly in a short amount of time.
Ashley started as a depressed girl who refused to express herself honestly out of fear, now she's quite happy and gaining confidence and has been shown multiple times to help others when they're down now. She saved Android from getting any worse for example. She went from helpless to helpful, and is now trying to save another person's life (Ms. Ren).
Maria is probably the best example from recent events. The hospital shook things up a lot, but Maria very quickly found a new purpose in rebelling and finding her mother.
It's always been my goal to take these broken people, get them healed, and have them use their experience to help the world. These characters would not be able to turn into the great ones I know they will be at the end of this story without being forged in fire so to speak. I think the hope is there, but it's not exactly where you expect it to be.
I would guess that Harem Hotel's story is about 60% done. More than half of the main characters have moved into the stages of "Helping the world" or are moving into that stage now since many of their isolated personal problems have been dealt with and they've been able to grow as a result.
And there are many holes in Syl'anar's system! Which I would love to talk about.
The biggest may be the most obvious, yet the one that may go most unnoticed as well. Slave workers. Every single vital part of Syl'anar's society is run by elves, from farmers, to cooks, delivery drivers, etc. Just about everything that isn't scientific, artistic, or political. If it involves labor, it's probably done by an elf. (But they've revolted 3 times before, so this is shown to be not enough)
Another weakness, which is much more subtle, is that the bulk of Syl'anar's military can be disarmed with an extremely cheap and available material. Paint. Vanessa points out that throwing paint on a droid's head (Such as the police droids) will block their sensors. Or just spray paint will do the job. EMPs would also work, but that's not as available.
The rest of their strength is in the police force, which is definitely substantial, and always has been in their history to control slaves.
I should also point out that you have the only sentient android(s) known to exist, so that has to count for something. You're also in bed with Kali, and she has a lot of potential to do some damage with her skills and who she is as a person.
And another weakness, which is much more subtle, is that the humans in Syl'anar are in constant fear. They're fed both lies and truths about the imminent collapse of their nation/economy if elves are freed, or treated equally. The hate all serves a specific purpose, and that is to keep elves as slaves on a cultural level. But a nation built on fear is a very internally fragile one. (But we are just now starting to see the main characters effect the world after all)
There's more, but I don't want to keep flooding this post.
Most of the events you mentioned about the player character's character are from some of the oldest events not yet remade, which is the same case with Cornwall's slave training orgy event. I think what you're noticing is my less than stellar writing at the time.
As for how the manager acts, well, this isn't a sandbox game, this is a very linear story. The choices you make are flavor only. The choices you make help shape the character you insert to. You are still playing as a character, but that character is meant to be you, not the hero of the story. So of course he will help Lin, you don't need to click a button to do that. It's impossible for any game to be a completely full self insert, at least with current tech. In every self insert story, the character has some of their own agency. Oh, I guess aside from D&D! Unless you have a bad DM, haha.
I wouldn't be able to write every possible action to make everyone happy in every moment, but I don't think I need to make him a fully fledged main character either.