For TFTD it would be nice if there was conversely an option to make items Land Use Only, cant use them underwater.
Though I would like to make that apply to grenades there's other equipment that could work as substitutions to aquatic items, and could even be more effective.
For example the original xcom laser weapons, available right from the start of the game because the technology has become commercialized and they've been sitting around in lockers for the past 40 years. And a rocket launcher to supplement the torpedo launcher. But in order to have those available for use for terror missions or base defense they'd be taking up storage space so there's the balance.
With that I had an idea for special rules for artificially scaling up the weight of items when it comes to throwing (underwater) to avoid breaking game mechanics, but artificially increase their weight so you cant throw them far. Or imply they are fired from some kind of non-item launcher which gives them a limited range and arcing trajectory similar to the deep-one weapon (maybe all the grenades including sonic pulsers are hand launched mini-torpedoes that only have enough thrust to launch them in an arc).
