Azem.Ocram
King
Cruisers (1st upgrade to Gun Boats) should get a perk to fire torpedoes at any tile within range without a friendly unit with a different color to select if seemingly empty. That would mean that Cruisers could fire at hidden submarines (or any other hidden units) but would need to have the submarines within moving range to know where they are. Maybe upset aliens slightly if you fire at "Chelonia" alien whales since the torpedoes hurt them but cannot destroy them, though I don't know if aliens can be affected by basic resources.
Submarines and Patrol Boats are fine the way they are
Don't change them unless you want Patrol Boats stronger (more "built like tanks" but faster and without guns) and Gun Boats weaker (more of a "glass cannon" that strengthens with affinity)
Prosperity: free colonist should be replaced with +1 Specialist yield and "Mind over Matter" should just be straight-up nerfed (+4 Health)
Submarines and Patrol Boats are fine the way they are
Don't change them unless you want Patrol Boats stronger (more "built like tanks" but faster and without guns) and Gun Boats weaker (more of a "glass cannon" that strengthens with affinity)
Prosperity: free colonist should be replaced with +1 Specialist yield and "Mind over Matter" should just be straight-up nerfed (+4 Health)