I will see if I can clear up a few matters.
1) Prologue:
The game has a sandbox element, however for the most part it is story driven. The sandbox is really just to create more immersion in the universe created. As far as the game design, I had to ensure that all crew members were aboard the ship prior to implementing the sandbox elements. This relates to the creation of the ship environment (navigation screens) with all of the different combinations at different times. When I initially created 0.2, there were roughly 1000 of these navigation images. If I were to progressively populate the ships crew, it would likely have been 5 times this number.
2) Quest Tracker:
There will be some bypassed quests within everyone's quest tracker. This is perfectly normal and nothing to get concerned about. These bypassed quests are only very minor in nature and won't affect an understanding of the overall story. The reason some of these can be bypassed is that I didn't want to force the player to dot every i and cross every t in order to progress. Note that bypass quests are events that have already come to pass.
There is currently a bug with the quest tracker in relation to the side mission, it will auto fix with the next version. With most of the quests, I have a tracking variable which is 0 (not done) and 1 (done). With the side mission I also incremented this variable to 2 if you happen to have accepted the mission. I just forgot that I did this and messed up the tracker coding for this element.
3) Backstories:
To progress the back story, you just need to progress the main story. The first 2 will auto trigger and you just have to visit Kara in her room to get her second one, once you have progressed the main story sufficiently.
4) Kara and NTR:
It's nice to see that people are so invested in Kara, that they are already getting jealous of Rachel preying on Kara's naivety. Don't worry, there won't be any true NTR and with the next version you will get some more action with Kara. However please note, that whilst it is a harem game, the MC isn't the center of the universe for all of the girls and they each have their own motives / desires.
Xavster, would you consider just starting the player at the prologue so new players can experience the story organically or a least give players the choice at the beginning to skip the prologue or not without having the forced flashback recap spoilers. I think it would make for a much more enjoyable experience especially for new players. As it is now, I immediately exited the game at the computer screen and came back here to check if I had missed the prequel or something.
It's actually a bit of a double edge sword. The concern with throwing someone straight into the prologue is that is actually quite long and a kinetic novel, which doesn't really represent the real game. I suspect players may get 15 mins in and then get frustrated thinking the whole game is a kinetic novel. Quite a few players don't get around to exploring what is on the Captain's PC, despite me placing them at it at the beginning of the game. This is what happens when you give people freedom.
To be honest if I could turn back time, I would have done it differently. My first game, so I'm still in the process of learning. The map and hint system as well as the quest tracker are all a result of feedback about the game. When I first published v0.1, I didn't have the RenPy knowledge to create these, however this has since changed as my coding skills have improved.