I've tried to give most of the subs some mass and retain some sort for aerodynamics. Its heavy scifi so I have some room for the "this would be cool" factor, but visually I try to keep it grounded in reality and use things that make you think naval vessels. Most units use props for propulsion, the others use some sort of thrusters (like a cruise ship). Other things like conning towers, marker lights, hull patterns and bubbles help sell the illusion. Theres always a bit of suspension of belief you can use, you just have find that line.
The weapons are class based, a loose rock/paper/scissors setup. There are piercing weapons (think super powered fully automatic spearguns), torpedos and beams. Each of these are specifically suited to destroying units, cap ships or structures respectively. I think beams would work underwater with enough wattage. Most commercial ROVs use them for measuring things underwater now.
As I said before, the game is a mix of shooter and RTS. You pilot your Deep Submersible Vehicle (DSV) for the entire game (first or third person), theres no overview like a traditional RTS. You and your opponents (up to 4 players) spawn from your Command Rig. The objective is to keep it from being destroyed. There are NPC enemies that spawn from certain locations on each map, as you destroy these and any enemy units your Collector will travel to that location and gather the scrap automatically. This is one of the ways you collect resource points/money to build more units/upgrades. There are also resource deposits around the map that you can drop a beacon on to call down an Extractor.
FATHOM relies on a "beacon" mechanic most structures. You purchase the beacon from your Command Rig or other structure, once its completed it will drop out of the structure for you to pick up. You fly this to wherever you want to place the structure and drop the beacon. The beacon will fire a beam to the surface and shortly after the structure will drop down to the beacons location. This makes for some interesting games.... for example you can drop in a cap ship facility near a resource point or your opponents base and cut the travel time down, or plant a mine field over their capital ship factory. There are surface relayed weapons/ordinance that work the same way. You can beacon in minefields, depth charges and a beam weapons at any depth you can reach.
Like most RTS games, you acquire money to make upgrades and purchase better units. There are 4 classes of DSVs, several capital ships, 3 weapon buoys, 2 classes of strike craft, etc. All of this is complete and in the game at this point.
Thanks for the feedback, keep it coming!