But as you use the unity engine you can "easily" make water a 3d object, and thus it does not require any morphable 2d terrain
The 2d terrain could be used to define the boundaries, the water is then rendered first as a 3d object and the level interior over the water. That way you can code an entire different set of dynamics for 3d-water without affecting the 2d levels at all (and it being 3d, you could even do proper refraction). Not to mention that this would be a pretty good idea to do because you could just define where water spawns and it spawns in the levels dynamically, you could even randomize this then and remove water tiles entirely from the levels. And even better, you could connect outdoor water with indoor water levels, define "leaks" and "sinks" to the interior and thus create a fully immersive world.
It sounds like a good idea to me
And i am not saying this just to bicker. atm AVVW is fairly well done but it does nothing extremely well in the immersion and visual category, liquids, ambient particles (yes i know.. it comes when polish comes), debris and some more "physical" destruction would do wonders. Just because its 2D with tiles doesn't mean you have to forgo every interesting feature of 3d-engines. In fact you already did something fairly similar with the "fancy" clouds (which i think need a better particle sprite, hopefully its not hardcoded or a 1-pixel pixel shader ;p)
Well if not then thats ok but i really have no suggestions besides flavor right now, i can't really say what the game is gonna be until the current base is somewhat balanced and features are all in... after all it was quite like this with AI War...