Well, the undewater mission from GBL was created by a comination of things;
1) The scrounge file (which is what makes the cracks in the icy levels, rocks on the ground, or in some GBL levels, snow) of the underwater mission "PETESCRI" is a verticly slow-moving scounge with bubble .xel textures.
2) The pallete file that makes the colors of the level is unusual, it's made from a similar fashion of the light-amplification feature, only it's blue instead of green.
3) The gravity setting in the PETEPLT1 file is set to ultra-low gravity, that way players will get the underwater "freefloat" feel.
The only problem with making an underwater map like this is that the mechs used in that GBL mission, they were using .MEK files with very, very slow engines to compensate for the low-grav, if you had a NetMech mission like this, you would either have to have a type of KAM for that one NetMech mission, or enforce a rule that everyone would have to use something crazy like a 10XL engine. Otherwise, you would have people running at insane speeds, and that would just kill the feel of the level being underwater.
But that, I must say does sound a lot like a good map.
I don't know about the moutain type map idea though, you would never be able to make a map like that and be able to perfectly fit everything together piece by piece. (unless of course you were in a prison cell and had nothing to do

)