Now that I think of it, they seem to be directly opposite to each other. To start with, lets look at their colour scheme. The Vodyani is black and orange while the Sophons are white and blue. Plus, their ships are also constructed differently. Vodyani ships are straight and edged while the Sophons are slightly rounded. Following their appearances, the Sophons are much smaller compared to the Vodyani. Now, you can say that they are both cyborg looking, but if we compare their original apperances without any of the tech and stuff, the Sophons are skinless and almost lizard-like while the Vodyani are furred and mammalian. Plus, their idealogy seem to go against each other. The Vodyani being religious and the Sophons being associated with science.

Looking forward to what people would say, thought this would be interesting to know.