Conceptually, I haven't seen anything like this before (especially in RPG Maker) and it really pushes the boundaries of what you can achieve in said engine. I found the space navigation a very immersive and enjoyable experience and you executed what I would have called a difficult to implement concept pretty flawlessly and the end result is fantastic.
In a way though the amount of innovative mechanics is almost a double edged sword as your gameplay style is so different that to get fully invested one would have to sit through a whole raft of tutorials just to get an idea of what they are supposed to be doing at any one time. Given this is a game made for a game jam that can be played in browser, I don't think I would really have enough time to invest in that myself, but I am of course only speaking from a personal standpoint.
It is easily apparent that you put many, many hours into this game and anyone with half a brain could see it is a very faithful love letter to 'ye olde PC games before the internet was a thing. I have to admit I did not spend a very long time in Mothership as the these types of games are generally not my cup of tea. What I was interested was witnessing the different game mechanics and other concepts the game had to offer. I was thoroughly impressed with what you managed to achieve here in RPG Maker in the time allotted and the wow factor was through the roof.
Congratulations on your project and thanks so much for making this game. I think the effort here was 'Stellar'. I don't know if that counts as a space pun by the way - probably not ;P