I think the deep-sea genre has kinda been abandoned, before it could be graphically realized. I'd like to see voxel water, or at least volumetric water of some kind, in a 3D environment. The idea that you're in a capsule in space and if there's a hole you die, is nice, but I think it's a very different image if it's a material trying to get in. You can actually see its progress, the deeper water affects your environment (can't open a hatch if there's water on the wrong side, have to wade and then swim, water making objects float so they're easier / harder to acquire).
The game could feature a slow breaking-down of the undersea base, meaning your opportunities for adventure get narrower as time passes. You could also include repair options where you can EVA outside and slap a patch on, then get back in and activate pumps to get rid of the water. The air necessary to refill the affected areas would have to come from somewhere - probably nuclear electrolysis of seawater - which adds another scarce resource or at least facilities to protect and maintain.
Most games that put you in the Space Plumber position (System Shock 2, Dead Space, etc.) seem to lead you along through scripted failures and necessary repairs. What if these were more randomized and the player had to keep track of what needed to be done? Along the way you're trying to do the main mission, and also deal with the monsters.
Let's say early on you're given a map of the base and the satellite areas that you need to EVA or take a single tunnel to get to. And you know the status of these facilities. The game tutorial tells you what to do to
repair a facility's hull - you need "weld plates" or whatever - and then
pump water out - you need to repair the water pump facility in that section - and
refill oxygen - you need either an active electrolysis facility in that section or else a complete air pump line leading to it
Do you have "weld plates"? If not, you need to go collect some. When you arrive at the water evac facility, it's clear the parts you need to replace. Do you have those? If not, you need to go get them. At first you may need to do a lot of EVA in a suit to gather materials, and slowly start reclaiming parts of the base that you need the most. The more you reclaim, the more danger of some part getting damaged again because there's more to go wrong, but your travel around the game world is easier, faster, safer.
Assume that the whole point is to reach, repair, evac, and air-fill an escape sub. You also need to reach, repair, evac, air-fill, and repair a broadcasting facility to request a pickup by a rescue boat on the surface because you're in the middle of nowhere.
Throw in some deep-sea trench aliens, some crazy crewmembers, competitive Soviet / Chinese / whatever scientists, and dangerous natural sea life.