1. Quests
An overarching story to start with. Like the current story kind of does. Its some sort of grand introduction.
In the meanwhile the guild and grand company stories will carry over, for i think that that's where the meat of the game is. Perhaps its even easier to expand on those two instead of having a expansion every 2 years.
For sidequests, i prefer it to be in tangent with the main stories, but i really dont mind some free form there too.

2. World story
I would like it at the base to be about development. Like making the company grand or maybe yourself can become a leader of sorts. I like your idea of elements, but the hatred part isn't to my liking per sé. Why not make it into different stories, and leave the hating to the players lol
Maybe the cities could be at the base of the story, because they seem to be kind of young, in spirit i mean.