That's an interesting thing indeed. I've always wondered how did they look like. Lol, maybe the Vasudans know 
Their civilizations existed next to each other for at least 2000 years. Pity that V never drilled the Ancients plot deeper.
They planned for FS3, but as we all know... FS3 was never made
.
I mostly think about ancients natural habitat as oceans of water or maybe other liquid. On the other side, life on alien planets may look totally different than on Earth so the Ancients should not be treated by our human measure. The Ancients may be non carbon-based species as well[silicon maybe?]. Knossos is the only shown example of their technology and architecture. I found jump gate as something fishy, covered in carapace-like materials or crystal structures so the natural association are oceans or perhaps other liquid-based habitat.
It's hard to imagine something with only one strange device as example of their technology. I doubt if we can be even close to official vision of V without further information.
