Just because he is powerful enough to unleash something like that it doesn't mean he has to do that. Of course he has never used a Super Nova. Otherwise there would be no Happy Ending. Look at all the anime villains. Every idiot is able to destroy the Solar System. Cell just needs one Kamehame-Ha - but he was stopped before he could. Broly needs one move to destroy the galaxy. But he was stopped before he was able to destroy the northern galaxy like he did with the southern. Anime villains are riddiculusly powerful. Most of the Final Fantasy villains are typical anime villains. And when your true question was "Why would he use a Meteor if he could use a Super Nova?" - Sephiroth needed a body in Final Fantasy VII to absorb the lifestream. He needed a point where the energy would focus and where he would be. So destroying everything and all the JENOVA cells so he wouldn't even be able to reunite himself would be quite stupid.
And yes, Xemnas attacks do not break plot rules as well. He was nothing but an example.
Maybe you think Sephiroth is not that challenging but in case your team heals him with Megalixirs over and over again because Super Nova has worked you'll probably think the same way I do about the battle.
EDIT: I just want to mention: You are right, there are things in Final Fantasy which are not logical. But the story of Sephiroth, how he combines his powers and everything is written and explained very well - there are some strange things about him as well. Indeed. But almost everything has an explanation.




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