Wow, awesome job! I love how polished and complete your game feels, and the art style is really cute!
At first I was a little bit confused what the flares are for, but as I played through your maps it became clear that flares are needed to keep track of locations and landmarks. I think it's a great idea to help players explore and understand the map on their own, especially when there is no space for mini map.
And all of this works really well because of the great map design. The fact that you can't see a lot of the time also adds to the mystery and keeps players engaged as they try to find the scientists.
I really liked your take on the submarine exploration theme, and I might have to borrow some of your ideas for my own game :)
If there was anything to nitpick on, I think the submarine's lighting state sprite could be slightly improved, the little dots coming off of the submarine follows the submarine too perfectly and doesn't feel like light rays. But otherwise I think the game is superb.