I just played the latest version for a bit and here are some of my opinions:
New ship design is decent, but I really dislike the uniforms. I know what this game is about, but "uniform"s being this slutty detracts from the more grounded science fiction side of the game. It can still be sexy without being this revealing. Let the uniforms just be sci-fi uniforms. There should be standard for uniforms when it comes to a ship like this, male and female uniforms wouldn't differ much, even if it is just a science and research vessel of some sort. Since they get out of their uniforms some time after the intro anyway, showing some difference between their "professional" uniforms and casual sexy outfits would make it better. Not to mention, players uniform (with helmet) seems to imply suits themselves should be air tight, which would make sense for sci-fi suits, but female version of the uniform have lots of holes, which would mean certain death for them in many situations. Not a good design let me tell you.
While the new intro is somewhat better at places, I think it is much much worse in others. For example, ships captain Adrianna is being too familiar off the bat is just bad. I feel she should be a bit more professional in the intro, she should make the player call her the captain and only loosen up after the passage of time. She shouldn't just go and hug the player out of nowhere when she doesn't even know him. Adrianna being so familiar with the player from the beginning takes away from what I liked about the game the most, seducing and corrupting her little by little. Since she is a married women she should put a little distance between her and player at least at the very beginning. After the intro player could mention something like "captain really warmed up to me over time", so it can be a little more realistic interaction. Same goes for Natasha, she can be a little slutty and tease all she wants, but not towards someone she just met, these things should happen after the intro. As for Katherine, you are revealing too much too soon. Working towards something have meaning, what you did there is more like fan service, before fans even exists. She should at least have her top and it should be a split second thing. Player shouldn't say "I make a mistake" for this event when it is not even his fault. He should say something like "it was an accident".
This might not be very important to most, but what is talked about the seeder in the intro is called terraforming. It should be mentioned as such.
Natasha always holding the top of her breast is plain weird and not in a good way. It doesn't help that their tits are comically, unreasonably, idiotically large.
As I said, none of the girls (thats including Natasha) should act so familiar with the player in the intro. Additionally passage of time should be more than just a month so there is an excuse for the familiarity between the girls and the player.
Player filling the system 30% unassisted at the first try defeats the entire story. Story should about "it takes a long time and I can't do it alone" kind of thing. They become willing to assist him because it would literally take years if he tried to do it alone. I mean, it could have been 10% and girls still could say thats a lot, given the size of the machine. It would be more convincing if nothing else.
New casual clothes is a step backwards. Not everything needs to have a deep cleavage to be sexy. Adriana's number 1 casual outfit is proof of this. Natasha's new casual out with her gigantic bra sticking out looks funny if anything. Again funny but not in a good way.
Lastly, there are many many spelling errors in the game. For example, masturbate was written as masterbate many times. It would be nice if you could use a spell checker. Also, there should be a dot after every sentence.
I have so much more to say, but this is it for now. Thank you for working so hard on this.