As discussed on IRC it could be good idea to explore possibility of ditching water tiles (not completely, to be backwards compatible) and going for simply setting sea level, or something like that. But it wouldn't be able to satisfy all users since it would mean end of individual levels for different water bodies. And making individual sea levels would be insane.
So the only idea that I could think of would be to add some kind of fluid dynamics to game engine, so we could get it done right. Then we would first create terrain and then use some tool to spill specified amount of water to specified place and let it filling so long as we get body water that we want. Which such system we could get "natural" water flow, proper rivers and waterfalls (by defining sources producing water at specified rate and kind of black holes to consume it, to avoid floods

Such thing would require lots of work and change way how maps are done but would give lots of possibilities, just imagine scenario when you must fight with enemies to control shrinking land area due to progressing flooding or maybe even things like enemy destroying dam to generate tide to destroy enemy base (I was always curious what would happen if we would be able to destroy that dam in beta campaign).

Also we could add ability to specify (maybe also predefined as sets, at least on map editor level) fluid transparency and color, or texture and particles for surface (water? who said water, I want acid and lava!

One more thing that could be cool, ice, especially if we would get full support for weather conditions.
There are also open questions, like what should happen to submerged structures (except that they should stop functioning after turret is submerged), should they be damaged only or completely destroyed (that would be most convenient, with custom animation, so no fire underwater

What should happen to them in case when water level would drop and they would be no longer submerged, would they need to be repaired first or automatically become operational (but keep previous damage, just like "touch to make them alive again")?
Or how to deal damage in case of tide (completely destroying structure wouldn't be natural enough), trying to calculate pressure from given amount of fluid?