This takes a little bit of explaining so here goes. I think that a level should not have a massive, level sized water plane already in existence. It might seem easy and convenient to just dig down to the water layer to get a lake or stream or whatever, but we don't always want to have water at the same depth everywhere on the map. In Unity, for example, you can plop down a water entity and scale it to whatever size you want and place it at any elevation. This would allow for lakes on the top of a mountain as well as having deep dug out holes with no water. The possibility also arises where you can change the properties of each water entity to give it different colors, different wave speeds, etc.
System Specs: OS - Windows 7 Home Premium 64-bit SP1, CPU - AMD Phenom II X4 945, 3.0Ghz, RAM - 8Gb DDR3, GFX Card - 2048MB NVIDIA GeForce GT 640, FPSC-R Version - Beta 1.0071