1. An option to change load-outs between "Surface" and "Underwater" options before taking off.
2. Weak Laser weapons and VERY expensive Plasma weapons (Elerium is not cheap) for surface operations; Air-to-Air weapons for our flying subs, for when you think that that USO is going to fly over land.
3. Specialized Surface and Underwater versions of items: With no need for underwater life support "Surface" versions of Armor has more protection; Weapons that can operate both on surface and underwater can sacrifice one for better performance in another, etc.
4. Swimming in non-Mag.Ion Armor: Can "fly" a certain number of tiles, regardless of time units, before "falling", and you fall slowly (one level downwards per turn if the soldier does nothing, or fall one level every time the soldier moves)
-Can't swim in starter armor, because that hastily created armor is too heavy.
-Aqua Plastic Armor: As explained above.
-Ion Armor: More heavy than Plastic Armor, but still lighter than the Starter one.
5: Alien outposts: One-parter versions of colonies.
6. Optional, but desirable: New Terror sites: Coastal Towns, South-East Asian water villages, Gritty Asian "Venice"-like places (as seen in Ghost in the Shell:
https://www.youtube.com/watch?v=c26iiSfC6Us Gits) and Venice itself.
EDIT: 7. Underwater Grenade Launchers, and to make it impossible to throw grenades underwater.
EDIT 2: 8. Additional door on the right side of the Triton.