I like the idea and I think the game has a good presentation, but there are some issues that stop the game from being enjoyed the way I think you wanted it to be.
Starting with the art I think everything looks good and fits together well. The particles are a good edition that make things feel more alive (although I think the smoke behind the ships feels a bit too big). The title screen is very clean and gives a great first impression to the player. My only real issue with the art is all the default Unity UI. It doesn't really fit with the rest of your art and gives off "placeholder" vibes (It only takes a second to draw a custom white box with a black outline). As a final note, I think the numbers on the ships were a good idea but they cover up the art a bit to much.
Next I want to go over the audio. I think you picked a very fitting song for both the title and game sections, although the scene swap when hitting start game is quite jarring. I would suggest adding a fade to black and having the audio fade between the songs for a much cleaner feel. In regards to sound effects, I only noticed the ones when ships move and the upgrade is ready. Its a good start to giving the game some life, and I noticed it does get louder or quieter as you move the camera closer/farther which is a nice detail. My only suggestion would be to add more sound effects to things like shooting, terminals opening, buttons being pressed, etc.
Last I want to go into the actual gameplay. Like I said before the concept isn't bad, but due to some issues I don't think the game is the experience you wanted it to be. There are a few bugs but you already mentioned them on the itch page so I won't go over them here. First off, The game has a lot of controls and none of them are listed in the game (unless you count the numbers on the ships). I know they are on the itch page, but I strongly suggest you don't rely on that. If you don't have time for a proper tutorial, I would say even throwing them on the bottom of the screen as a static UI element is better than nothing.
Next, I think the main concept behind your game is ruined by the fact that it is completely optional. From what I can tell the best way to win is to just attack the enemy ships on game start, ignoring the upgrades. I think a solution to this would have been to make ships respawn, and make winning only happen when you destroy the big red ship. Then maybe give the red ship its own guns to protect itself so that you need to upgrade a bit to actually take it down (this is just one idea to make the main mechanic more necessary, but I'm sure there's many ways you could have done it).
Overall the game is still interesting to mess around with for a bit, and I'm sure with more time many of the critiques mentioned above would have been fixed. I'm glad to see you tried something new, and you've improved a lot since the first games I saw from you. I apologize if this review was a bit much, but I'm doing this to all the games from this jam as I think critiques help us grow.
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Thank you very much for the detailed feedback! I will use it and do my best to iterate on the game to make an enjoyable simple RTS that requires a bit more strategy to beat. I definitely ran out of time with this game since I planned it out with an expectation of about 35 hours to work on it and ended up spending only 23 hours around the New Year holidays (and 3 dnd sessions) this week.