SE is a large company but the game still has a budget and more importantly, a schedule. It can't just have its story continue to balloon out of control with tons of plot altering choices. That will slow down development, and working those choices into the actual game would take time away from actual features. While I do wish the FFXIV team got more to work with, you can't isntantly solve all the problems by just throwing money at it either.You're really underestimating how much work these decisions would be in the long run.
As I said before as well, FFXIV is a multiplayer RPG. For the sake of RP, I think it's better for this game to have one singular linear narrative anyway. Because then when people RP, they're rping in the same world, with common ground. Rather than one person RPing in a world where the WOL was a hero and other people rping in a world where they sided with one of the bad guys and conquored/destroyed Eorzea etc. That would just divide up the rp community and make things needlessly complicated.
If you're wanting a game where you can side with the bad guys just to screw the world over, just for the sake of edge and darkness, that's not going to happen.
I love the opnness that some games like Fallout or Dragon Age: origins give, or the freedom of D&D restrianed only by the imagination of the DM and players, but this is not the sort of game where that's going to work.
Maybe if each expansion had a stand alone story it 'might' but with its ongoing story from one expansion to the next, with many of the same important characters, and often going back to old areas, it just doesn't work. Like, how could you have the restoration of ishgard if half of playerbase sided against nidhogg and burned the city to the ground and there was nobody left to rebuild? How could you go on to fight the garlean empire if Emet turned you into a light warden? How could Zenos be set up to be a big bad again if you turne dhim into your Vegeta esque side kick?
I'd rather just let the writers tell the story they want to write. I can get my decision making affecting the plot elsewhere.