Overall epic game
This game you have created is absolutely amazing. Amazing storyline, great music, and some things mentioned in the game give you meaningful things to think about. There are a few things I'd recommend working out a bit, though.
As some people have mentioned before, this game got rather repetitive .... I'd like to see new/different bosses at the end of each level. But I loved the story behind the whole game, absolutely blew me away. I would suggest listening to what some people suggest and make the dialogue more interactive or add some more features to the bridge, like instead of clicking on several bars, you could have an elevator or room to use to select different destinations within the Mothership which would also give you a chance to show new/different graphics.
Controls were pretty easy to understand, and easily accessible. The characters seemed to have been developed pretty well, my only suggestion is to perhaps make it possible to talk to all characters when inside the cafeteria instead of just 2 people. You did a pretty good job with the weapons. I say 'pretty good job', because i thought maybe you could try to balance it out? I don't know, it just seemed off throughout the game. I really like the soundtrack. It really matched with whatever was going on, and I completely enjoy listening to it.
Overall, this game was put together amazingly well. You've managed to make an amazing combination of an RPG shooter with visual novel dialogue and a touch of sim dating. One of my favorite games, for sure.