It's a fair observation. Thanks for taking the time to provide a write-up. People think that creators don't want to hear things like this, but I'm really grateful for the fact you took the time to play the game and share your thoughts.
Sagacious-6 isn't a deeply complex character and I can't say that he goes through a character-arc in almost any of the branches. In fact, he's downright nasty, a deceiver and sees people simply as a means to an end. I play that consistently in every circumstance he finds himself in. Stellar Incognita is a story that goes wide (scenarios) instead of deep (story progression and character study). But there are future updates that deviate from this formula somewhat. The game was never meant to appeal to everybody (impossible) or even broadly. I do however, want to find a core audience for this kind of pulp-trash escapism with a heavy emphasis on particular fetishes.
On the other side, I am also acutely aware that Xandra is quite a passive character for the most part and serves as a support for whatever scenario Sagacious goes down. First and foremost, Stellar Incognita is a fap game that shouldn't be deconstructed too deeply (because if you did, I think it could become too grim). It would be reasonable to say all the characters are two-dimensional caricatures. Having said all that, Stellar Incognita and 8 Days with the Diva are teaching me a lot about Ren'Py and designing games. The third project I am going to make will add a lot more range as to the kind of protagonist you want to be, from nefarious to noble.
Oh, and thanks for the compliment on the artwork choice. I was going for something like this (probably didn't succeed):
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