Well, to start off with, let's point out that, even if Aatrox won out against Mordekaiser, there wouldn't be anything there for him to really control. AFAIK, all that Mordekaiser is right now is a wrathful presence and a suit of armor. Aatrox makes his form by sculpting the flesh of the victims he dominates, so he'd probably be at a loss when there's nothing there to give him substance.
That said, it's probably reasonable to say that, in a battle of wills, at the very least, there would be a stalemate. Both Aatrox and Mordekaiser are indomitable warlords hell-bent on something, be it Mordekaiser building his realm of death and securing his eternal unlife, or Aatrox's inconsolable rage and determination to destroy all things.
But that's at the least. Ignoring the possibility of another Kayn scenario where the scales are tipped only as a gameplay abstraction, I'd probably put my money on Mordekaiser winning out. Aatrox may have that single-minded, self-destructive goal in mind, but his imprisonment broke him, and he languishes for a life that once was, and an end that may never be. Mordekaiser, on the other hand, is probably very, very well-focused, and he's clearly powerful beyond measure, considering that he can manipulate the Black Mist.
And with his ambitions not being held back by distractions like longing or tainted by rage, he'd probably be able to quell Aatrox's resistance if he were to pick up the sword.
Though, that's just my take on it, so take it with a grain of salt.
