There aren't enough bosses to cover for all overarching stories.
I received criticism like this before. Some people enjoyed, others didn't like it. It is what it is.
SC has a lot of information and stories that will connect. From your brothers to even another planet survivors.
If your answer to a complaint is "it is what it is," then your PR guy needs to be fired, the writer needs to be reined in, and the lead developer needs to take a course on office management. You know what happened when nobody criticized George Lucas and let him write what he wanted? We got episodes 1 and 2. Lucas hopped at ideas he had and nobody had the balls to tell him that an idea was bad.
Your story can be an instant classic, a Shakespearean masterpiece, but guess what? Unless you "cut the fat" that people are complaining about, it won't be read. Right now, a majority of the positive reviews are the kind of empty praise that comes from people who actually think that Rick and Morty copypasta is some kind of deep, insightful statement. It's a shitpost, but they're all too dense to realize it. Those are the people who gave you five stars and claimed your game is some work of art. That is the standard you have decided is sufficient for yourself.
Now, I did give you some advice on a certain scene. The scene where diplomacy is in action, that isn't necessary. Have the Hunter sent that way reacting
after the fact. Give us insight into how this society operates without showing us the boring parts. Politics isn't interesting. Star Wars can tell you that. Neither is two dudes talking about the recent past.
Rather than that scene in the room where the Embodiment of the Sun reveals what really happened, instead have the scene where they meet and then cut to them standing atop the gate and have the reveal happen. It works more fluidly if we don't have downtime before the Hunter in that scene is thrown into a frenzy and looking to murder something.
The stuff with the succubi homeworld is more fluff than relevant. You could argue that insight into the villains helps flesh things out, but I honestly couldn't have cared if Domina was an mlp fan character or a Lisa Ann image insert. Her and her forces added nothing of substance to what was already stated prior.
The other dimension stuff is also kinda irrelevant. I would honestly save it for when you meet up with them, and significantly shorten it to a handful of stills for the flashbacks. Let them exposition dump for maybe 5 minutes and move on.
I can't salvage the stuff with the mute Hunter. The best I can offer is he gets imprisoned, then the next scene is him sneaking around and confronting the mob boss guy.
Your cutscenes just got reduced to three main story ones, and a quick flashback later on. Problem solved, and none of them need more than 5 minutes to say what they need to say. Oh, and the Domina scene is gone because it added nothing except a cg. Yay. A single cg. You paid $40 for that, maybe?
I just edited your story for free.