Physically: they're both pretty much unstoppable, so no advantage there.
Lightsaber skill: Krayt performed well against a post-ROTS Kenobi before improving drastically over a century. Kun stalemated Ulic Qel-Droma, prior to obtaining the Dark holocron, in which he discovered ancient Sith lightsaber combat techniques and improved drastically in skill. They're about equal, but Kun has the form advantage, as a fellow master of Niman/Jar'kai techniques and having adopted a style Krayt does not know.
Force: Both are incredibly powerful, but Exar Kun has edges here and there, as well as a large margin in terms of Force knowledge.
Hax: Krayt has Dark Healing, Kun has Force blast and Tendrils.
The fight is as close as it gets but the only edges I see are margins for Exar Kun. I'm sure others disagree.