The biggest flaw of that "fundamental" system, where crafting classes are supposed to be classes just as the Battle ones is...there will never EVER be anything like CoP again, ever. Crafting classes are supposed to be able to get all "Story Quests" done, just like Battle Classes...which makes challenging battles like in CoP completely impossible.
The fact that so many people liked CoP and still think it was the best storyline in FFXI so far(and prolly will be forever) was not only the storyline itself being really good, but it was the whole "effort" it took to actually experience it.
Something like this will never be in FFXIV ever, when crafting classes stay the way they are.
I do craft myself...I do it a lot actually...but crafting classes being part of "Main Classes" is just limiting the content they could implement for Battle Classes and wether you like it or not...the majority of the players still play Battle Classes over Crafting Classes.
The ONLY option right now to get something like CoP in the game and let crafting classes stay the way they are would be, to implement 2 different Storylines for Battle and Crafting Classes. Battle Classes should experience the Storyline from a more battle involved perspective, while crafting classes could experience the Storyline from a more "supportive" perspective, for example there is a big battle going on between the Garlean Empire and the leftover nomads from Ala Mihgo. Battle Classes could be directly participating in that battle, while crafting classes experience it from the "defense" line and craft stuff for the nomads battling on the field or anything like that. Make the Storylines reward different things to match the Class you're playing it with(just like the CoP Rings for each class, just make it crafting/battle/mage rings for example)
The only reason I want to see crafting classes being treated as what they are, is the fact that it would ruin the possibilities for the storyline when it comes to challenging fights.
PS: Do you actually play FFXIV? Cause there is no character shown on the Lodestone on either Sanctus Refero, or Origami Kitsune...