Lavos may be gathering his power, but he is a terror even in prehistoric times. When is he at his most powerful in battle? At the ocean palace. An interesting thing, and leads me to believe that even in ancient times he had great power. I have never been much in favor of the entire idea of Lavos being a parasite and evolving and such. To me his is and always be a Dark Lord of a sort; boundless in evil and malice. I know it may be said that this is a great extrapolation and is but a loose opinion and is certainly not what was originally intended by the designers. I must stress, however, that many of the discussions pertaining to the timelines and origins of certain things, etc. that are discussed here are also but extrapolations and theories based on evidence, and likely do not coincide with the designers original intent. So please treat this idea with as much validity.
This being said I think that Lavos would defeat Sephiroth at any point. I have yet to understand what the fabled might of Sephiroth ever was. Interestingly the intent of both Lavos and Sephiroth was the same: both strove to drain whatever energy was in the earth and thereby grow stronger. The difference is, however, is that Lavos succeeded; Sephiroth did not. Sephiroth, though containing some Jenova DNA is still intrinsically human, whereas Lavos never was, and was in origin immortal. He began mighty, and died mighty. Sephiroth was never so powerful. To destroy worlds was Lavos' existance and being, to Sephiroth it was a goal he bethought only later. I would rather equate Sephiroth and Magus like in power; both may be seen as dark magicians, wielding great power and terror. They, I think, would be an even match. However when Magus summoned the demon Lavos to his fortress, he was defeated; only the timely intervention of Crono saved his life. So I maintain that Lavos was and always will be the mightier. Only through success of his meteor project could Sephiroth have hoped to best him.