Would be cool that we start out with just building bases on land, and if the game has grown enough and is succesful enough, have a Xcom:Terror from the deep style patch which allows for a special underwater Mek, bases built on platforms on the ocean and with new kraken and c'thulu style kaiju to fight and such!
I donated too low to get the visual book so I may be talking about of my ass....
but since we are terraforming worlds and the 1st world setting is ice which slowly moves to the last of a lush world. I guess it would make sense to have mining/THMPR events underwater when that portion of the world unlocks.
It could make it interesting to see a whole list of craftable frames, modules, weapons, THMPR for efficient underwater events rather than using the normal omiframe. They could even do it exactly like what Aca9 has said. Let the normal omniframes be able to traverse into water but at movement cost. Which means they could mine underwater but it would be very difficult to mine for the rare stuff.
Yet again I feel the need to reiterate...Grummz has stated that he does't intend to have an large bodies of H20 anywhere in Em-8er. I am just guessing but any forest/jungle type terrain that gets created will probably have water drippers and such to regulate enough water to keep things hydrated without creating a lot of runoff. Water Condensers would pull water out of the air which would prevent H20 precipitation. I also suspect that environments which would normally require a lot of water here on earth are going to be critically rare.