I'd have to say lack of play-style balance, especially in the endgame.
As a tech specialist, I have NEVER been defeated, much less threatened against anybody except Janeria when I go pure melee and grab the B.D.S accessory from Badger. The enemy is either forced into maxed out lust in the following turn or in the turn after that, or I manage to beat them up enough that it also doesn't matter (sometimes if I stat train I can even do both methods of defeat). A shield boosted Tech Steele has about as many shield points as HP as some bosses do, and with rather easy to get items such as Vamp Blade on Myrellion, your only threat is a lack of willpower and simple bad luck. B.D.S itself is just a massive issue that allows for a easy experience for a Steele that took the Shield Booster perk. Even easier if you take the Ice Cold perk to make the teasing easier, which I find to be a weird perk considering it gives you massive benefits with no real trade off, benefits of which often beat lust builds from what I see.
I even went in with a Ranged Tech Steele built to destroy things against the ship in the Syri Quest on Uveto, and I found that a Tech Steele is actually able to destroy the ship with Sunsetter (bypasses shields). Not only should that have a line if dialogue if it's intended to be doable, but the fact that a Steele is in the first place able to destroy a piloted ship without piloting a ship nearly effortlessly, tells me that there's some genuine balance problems. Especially since Melee would've done the job faster if it could bypass shields, but the fight ends the moment you take down the shields.
Ship battles are moreover an inconvenience than an actual thing to worry about. It felt exhilarating the first few times, but when a couple well-timed shield/repair boosters that don't fail and reading the enemy's energy levels to determine the rough attack pattern makes all the encounters nearly pointless, there's not really a need to upgrade or get a new ship besides accommodating more crewmembers. Speaking of that btw, why are all the non-Tavros ships so damn expensive? I get they're powerful, but the prices for them make it look like they're just there for flavor, especially since the Sidewinder makes them all look pathetic, as it has the best stats out of everything in the game, and having Olympia along isn't even an issue. I often end up getting the Sidewinder before actually even facing a Star Viper, as the Sidewinder is just plain easier to get since you can often tease.
I'd rather just boost away every time I have a ship battle, because unless it's a Star Viper or I haven't increased my stats, I generally won't lose. Pretty much every Steele needs only 3 stats to begin with.
And perhaps the biggest problem is how the game's text tends to treat your PC as if they solely use their gun. Text should change based on how often the PC uses a particular attack choice, and so whenever I see my normally slash and smash Steele suddenly having their hands on that peashooter they had since the beginning of the game, it looks very odd that literal endgame bosses such as Janeria are being felled by it, when the Plasma Blade/Reaper Stun Baton I used is what felled them to begin with.
Other things, such as the Frostwyrm Good End not having any real in-game consequences (Personally, I'd like it if my crewmates would know I'm staying for a full Terran year in a dragon's lair to make Frosty hybrids.), or the rival effectively just messing around and not actually applying any in-game pressure/consequences. I get why there are no consequences due to not all planets being accessible yet, but I feel like the rival should have some dialogue in certain situations given to Steele should they take a long time on certain things, or you lose out on the Myrellion/Tarkus/Mhen'ga probes if you take too long, just like if you instead send Myrellion into Nuclear Winter and Dane texts you the codes because rival is visibly a poc.
I once got a message from the rival while they were trapped by the Nyrean Queen sending a pic of them being worshipped by Zil, just as I walked in the door after a whole year passed because of completely natural pregnancy... like, wtf, cuz? I gave you a year to escape, do you and Dane just like taking it in the butt? Were you even remotely curious when I stayed on Uveto for a whole year, seemingly having disappeared from society with the biggest ship from the powerful pirates of the galaxy? Have you even checked to see how that Frostwyrm Blood Vial had came into existence? I was literally spending the next 10 years minimum of my life preparing to rule Uveto with a hermaphrodite character with 3 wombs for maximum efficiency, all just to make an empire that'll dwarf my own father's company as his nursery goes either used somewhat or completely unused. You're even lucky the game's code doesn't factor pregnancy speed modifiers into the Frostwyrm pregnancy specifically, because if that was the case, you would've just had to given me less than that.