Nice images, they really help. I really like the idea of buoyancy for determining how things are laid out. It'll be a side-view 2D game, then?
The little characters look pretty adorable, makes me think of Sea Monkeys or Pikmin, with minimal individual personality. Your hut layouts seem solid, and without knowing what the purpose of individual structures might be, I'm assuming you'll have some residential pods and some industrial pods, maybe something for gathering and processing resources, another for training combat units, manufacturing goods, etc. Having different buoyancy values for each could make the process of upgrading your compound very rich, since you'd have some rocks hanging on the pods as placeholder ballast until you get your spear-works installed, which will throw off your weight distribution and compel you to rework a bunch of your balances.
It makes me think a little bit of
Captain Forever, a game I enjoy very much, despite being terrible at it.
With regard to combat, I'd expect melee combat to be more a grappling affair than striking, so your little guys might lock onto enemies and engage that way, and when one dies the other goes in search of other targets. A physics system for projectiles (if you include any) could be cool, and you could work the buoyancy angle into the fights by deploying ink clouds or toxins that alter the terrain of the battlefield, giving it a cool underwater feel. I'd also think about condition-based combat, where a shark could be introduced (intentionally or by chance) that would target wounded units based on blood, or a trained dolphin that your guys could ride, turning a spear into a lance and giving a neat charge attack.
Think about ways marine animals fight. Poisonous spines or bites, flappy bait tentacles, straight-up teeth, entangling sucker tentacles, piercing beaks, even exotic stuff like the electric eel's shock or that one shrimp that punches with a supersonic claw could be worked into the game without feeling weird.
Plus, the ocean's been enjoying natural selection for a lot longer than the land has, so there are incredibly varied and sophisticated things down there. The environment shouldn't be made too sterile. Anemones, coral, various types of vegetation, urchins, all kinds of camouflage opportunities and caves and rock formations and whatnot could be thrown in as you find it convenient or fitting.
This seems really cool, I'm excited to see what you do with it.