So how do you categorise player into Disciple? I have both crafting and fighting >_> If they do, then they need to allow players to choose which storyline to play out. And like RedGalka said, you can parley in most storyline mission instead of fighting.
In that case you could do both set of missions giving you two perspectives on the overall storyline.
I'm thinking they could implement something along the lines of "Artifact Armor" quests, in the same fashion that FFXI had these quests. For non-FFXI'ers out there, Artifact Quests were storyline driven quests and battlefields specific to your ffxi job which yielded good gear (probably when they were introduced the best gear) when complete. There were 6 pieces of gear: Weapon, Head, Hands, Body, Feet, and Legs. I'm thinking they could take this deeper in FFXIV, what with the different guilds and such.
Also, this would be really cool for crafting classes, you could make the crafter run out to a place and obtain a rare material, then have to craft a rare item related to a storyline and the result would be some piece of gear that would help that class specifically.
That seems like a really cool application for crafting classes.
I would really like to see creative ideas/uses for crafting ranks. Your example of getting/crafting with a rare material is a good one. I also think that using the crafting mini-games to solve puzzles could be a good idea as well.