Lust SIN II is godly compared to the original, it really gives the vibe that Jin has found his purpose and resolves to live up to it. Especially the segway into the final chorus.
Awakening the Chaos II, because it shows just how batshit Nu is. It goes from calm and serene, but then foreboding with the child laughter
Plastic Night II, it gives Relius that much needed villainous vibe. Like, when this plays you know he's bad news. Dat opening.
Under Heaven Destruction II. While I have a soft spot for the original as one of my favorite themes(Especially the anime remix of it), the CP mix does a far better job of showing how to forces such as Jin and Ragna mix. Namely, they don't. One verse is guitar, the other is violin and then they come together in one last build up. Order vs. Chaos has never been so righteous.
Six Heroes, my god is this track god tier. Just what'd you expect from six of the most badass characters in the series. Really gives them that holy vibe.
Childish Killer II, like Shinwa said, it sounds a lot more dramatic.
Black & White, because Ragna & Hakumen were long overdue for a VS. theme.