I love the blue color palette and that everything sticks to it! The scrolling backgrounds also look great, though from time to time there were some black bars that appeared in them when I was playing.
The mechanics are very creative, it's fun to change the position of your boat, and you always have important fast decisions to make while in the level. Unfortunately it was often frustrating for me because I had three actions that did nothing to solve my problem, maybe they are all "move right" when I'm already at the right side of the screen. I would suggest making the swapping a bit faster or the enemies less numerous lol.
It was also often frustrating how slow the sub moves. When you have to swap abilities and quickly press the right one, you don't have a lot of time, and this could be improved with faster movement or swapping I think.
The music felt a bit monotonous, but also kind of fitting for the atmosphere. Could have used some more instruments, or a longer melody maybe!
About the art by the way, I would suggest sticking to a single resolution for the pixel art sprites, that ties everything together even better! Maybe google "mixels" to see what to avoid. Ideally you would also make the text and UI elements pixel art, but with the small resolution I see why you went for a different approach. Also it's a lot of art to do for one person :D
One thing that is unique about this game that I really loved were the crew members. There's so many different ones to choose from, and they have different abilities that really make a difference. Again nice work giving the player choices that matter. It's also nice that you can upgrade crew, though I wasn't sure what to do once I all upgraded them. Getting more money at that point is kinda pointless I guess? The designs of the crewmembers with their names and stuff are really cool though.
Overall a game that presents a nice unified experience that flows quite nicely. Especially impressive that you did this all yourself, including coding, graphics and audio. Very well done!