The crucial question here is this: Are we talking Human Darth Vader (pre-suit) or Cyborg Darth Vader (post-suit)?
In terms of Magic versus The Force, Human Vader has Sephiroth beat. Considering Starkiller was skilled enough in the Force to bring down an entire Star Destroyer, Darth Vader, Starkiller's master, should be more that strong enough to smash that giant Meteor in the sky down on Seph's head. I'd be inclined to think any other magic would go the same way; it wouldn't be hard for Vader to simply throw it back in Sephiroth's face using basic Jedi/Sith element channeling skills. Also, if game mechanics prove to be true to life, he should be able to simply reach out with the Force and pluck Sephiroth's materia out of his weapons and armor.
Combatwise, Human Vader could fight circles around Sephiroth. Anakin has been referred to many times as the Galaxy's greatest lightsaber duelist, due in no small part to his outstanding ability to anticipate his opponent's strikes using the Force. With the immense power he commands and the hate in his heart, Sephiroth is bound to stand out like a beacon in the Force, practically telegraphing his every move. Sephiroth's SOLDIER training might be formidable, but I doubt it could contend with a fast, strong Jedi trained in five forms of saber combat.
So if it's Human Vader versus Sephiroth... Definately Human Vader. Cyborg Vader, on the other hand... He ain't so lucky.
He'd still have the benefit of basic Force abilities (push, pull, grip) to deal with some of Sephiroth's spells, but his lack of an organic body would be a serious handicap. You see, the reason we never see Darth Vader using Force Lightning after his transformation is that he lacks organic hands, and therefore is incapable of channeling the Force through them. When he uses Force Grip, he's doing it with his mind; the hand gestures mean nothing. What this means in terms of combat is that any elemental attack Sephiroth could whip out (like, say, Bolt3) would utterly demolish Vader.
The "materia steal" option is still there, but I doubt he'd get the chance.
Combatwise, Seph probably has the upper hand. I would say that most Jedi sword disciplines could best whatever Sephiroth learned in SOLDIER, but since his body is 90% robotic, Vader doesn't have the luxury of those disciplines anymore. He's limited to broad strokes and wide arcs, leaving him severely limited. He might have been able to go toe-to-toe with Sephiroth once before, but now he wouldn't have a ghost of a chance.
So, if it's Cyborg Vader versus Sephiroth, Sephiroth definitely wins.
