Tangible factional divides are a pretty terrible inclusion unless the game is built like, from the ground up to be basically entirely about them. And even then, there's a low of ways to blow that; WoW's gone on long enough to have run into most ways to screw it up by itself, including the ways that contradict other ways.

If you just include factions without going through any meaningful effort to differentiate them, be it in gameplay or story, then it just won't really matter. It'd be like the grand companies, like Eclipse said; if all it really changes is where you do faction turnins and what icon appears on your character sheet, then it ceases to be meaningful beyond what color your rewards are, or minor metagaming situations like 'the Flames have the closest HQ to an aetheryte'. We've already got that situation, and you most likely already ignore it, what would adding another, more moustache-twirly faction add if that's all it is?

Now if you want to big it up, that's an angle, but again it's an angle that basically needs to be game-spanning to reach a point where it actually matters. That doesn't necessarily mean every faction needs to have an entirely different story--The Secret World got pretty far out of just crafting a handful of faction-specific cutscenes and quests and having all the mission turnin texts be faction-specific, most of what unfolded was identical--but in FFXIV's case it would kind of have to be, because there isn't really any smaller component you could change out. Swapping out the 'HQ team' sounds largely plausible for A Realm Reborn, then you've landed in the TSW situation where you swap out the Scions for different people, but... well, you don't have to think very hard to notice that idea gets progressively more impossible the further you go in the expansions. For that to function in FFXIV you'd basically be writing two mostly different stories, and there you run into another problem with factionally-divided MMOs: they're always super lopsided. I remember at one point, a City of Heroes developer got asked why the villain side tended to get less content, and he responded that only about 20% of the playerbase actually played villains. Once the numeric divide comes in, it's going to quickly become clear that working on one of those stories gives significantly less return on effort invested than the other, and at that point, you're gonna start writing with that in mind, either by half-assing the minority faction's content (what CoH did), writing overall content that favors the majority side (what WoW did), or just not bothering to do the faction-specific content entirely (what TSW did).

Also, I'm tired of playing MMOs with that factional element. If I wanted to keep playing those games, I would be; I'm here in large part because this game doesn't have that, and I find the community largely better for it. I feel like the factional element does weird and unpleasant things to the playerbase of an MMO with it, particularly the roleplaying side that I tend to get into. Either people take the factions really seriously and start treating people like crap for daring to pick different from them (or the sub-type, 'a portion of the playerbase picks the Obvious Bad Guy Faction and then use it as an excuse to be dicks'), or the playerbase just rejects that side of things at all and often scorns the people who do try to bring in that part of the game, despite it being... y'know, a part of the game.

So yeah. You can't just 'bring in factions', doing so would be a terrible idea on basically every level it's possible for that to be a terrible idea.