The story isn't 'confusing', it's just very, VERY poorly told, requiring you to look up datalogs and studying the in-game encyclopedia to understand 90% of what's happening. You shouldn't have to do homework for a game, especially not a JRPG. Dark souls gets away with it becuase the point of Dark Souls is atmosphere and gameplay, but Final Fantasy's story has always been super important.
I understood the story the first time round without these but it leaves a very bad taste in ones mouth without all the necessary world building. Comparably every final fantasy before this sewed every ounce of the world into playable and story segments.
Although FFXIII is a masterpiece compared to the aweful story telling FFXV which relies on entirely separate pieces of media like the CG film and anime to build its world.