As for one, Sephiroth is dependant on the JENOVA cells in his body. Without those, he would be pretty... Weak. Even more so, Sephiroth is mainly mortal, where Ian is... Less mortal. I think Seph would die sooner in a battle between the two of them.
And, Ian could always steal Seph's materia, so he won't be able to cast Fire3 on him.