I'm not sure what the big deal is. While Lightning isn't the main character of FFXIII-2, she is still a fairly important character in her own right and basically kickstarts the game by motivating Serah to go off on a journey.

You have Noel and Serah as a pair throughout the game, but you also have Caius and Lightning as a second pair, fighting their timeless battle. Having the main villain and deuteragonist on the cover is pretty par for the course for FF logos.

And they're only logos, they're meant to represent a key aspect of the game. Serah and Noel are important, yeah, but Lightning's and Caius's timeless war against each other is a central theme of the game.