With Water Comes Swimming, With Swimming, Diving.

[MorioMortis]

I could see underwater bases and passages as a possibility, like the caves in PS1, and depending on if (and how) swimming is implemented, maybe with flooded/fully submerged sections. Maybe even some small water crafts and submersibles.

However, ships really don't fit in the game, as this is about a conflict between three factions on another planet: if the VS or NC make warships of decent size, they'll just get OS'ed to oblivion (the TR maintain most of the control on the fleet, including most of the military stuff spaceside), and if you have the resources to do so, why not make spaceships instead? I mean, today, the viability of a wet navy (and even there, only carriers and their battle groups) is debatable as anything but an advanced base or, in the case of submarines, for surveillance and, more importantly, as a tool to increase the operational effectiveness of nuclear weapons.