Okay porn VN and all that, but this thing is a pale shadow of Unending Void over backstory, consistency and good writing.
Most glaring.... what's the point with Alex? Is he locked in the inaccessible cockpit and only able to send one SMS thread the entire VN with a cameo appearance once or twice? Was the author going to use him for some possible cucking, ntr, swinging or bi-curious fun and then chickened out? He doesn't even rate as a Star Trek TOS redshirt to get killed every planet fall only to be resurrected in this thing's version of a Space Engineers survival kit.
Military Discipline is non-existent as others have noted. Suggest author binge watch the Michael Moore Battlestar Galactica series and practice having the MC refer to himself as Agni Actual on Comms until he starts getting the idea. Sending out a bunch of first timers in their own ship without having any seasoned vets as mentors in higher ranks is absurd. Even if there is some sort of corporate treachery going on that caused this to happen, there's too many checks and balances from competiing political groups that there wouldn't have been immediate blowback. Aslo where the hell are aliens who set us up with the tech in the first place? They would have had at least one representative coming along for the ride.
Space Time and the known universe here is messed up. Just how fast is the ship and how far is the extent of the exploration going on here? Are we popping over to Proxima Centauri to buy milk and eggs, and, if so, why is our new crewmate having such a hard time finding and getting back to her home planet? The author may want to consult some astronomy referrences to get names of star systems that are somewhat familiar to space opera fans.