Well there are more reasons then choice for what I suggested - but also keep in mind I suggested all three.
Normally I try to be more specific for what I suggest but honestly all I want to see is jobs be their own ideinity like -everyone- here is saying. I dont care how, I just want it to happen. I saw this as 1 of the many ways you could do it.
Now the reason why I suggested this one is because Jobs MUST take some of the classes skills like what is a WHM without cure? Well that's in CNJ. So WHM must take some of CNJ skills but you dont want all of them - and how do you tell the players which ones are coming and which ones are going. On a really long tooltip? Soulstone information is 5 pages long? lol I didnt think that was a good idea.
So I said what if we made it visual. Here you could see the WHM Diverge by taking new abilities and passives, and converge by taking old class skills. When you first start the grid, sphere, thing, you will have some of it pre filled out - this would explain the basisi. And the growth would help maintain logical coherency on the growth of the class. (Not only would this help explain gameplay mechanics but you could make the gameplay mechanic itself fun as well as the fact that it fits in nicely - since the soulstones are presumably solid aether similar to the aeteherytes.. so its like you are growing your special materia that captured the soul rather then the experience of an event)
Otherwise you will have random spells coming in and not coming in and players will be like wtf? Also using this grid allows you to break some rules like adding weapons and such (all you would need is a sphere equipped so it doesn't change you into another class).
Now in the Crystarium and the Sphere grid you have great opportunity for choice and act like real talent trees. But that wasnt the main point of my post. I like choice, I like making my choices and yes as many pointed out its hard to design multiple choices rather then one best choice (but when it happens its worth it).
All I care is to logically explain how the jobs can separate and yet lay dependent on, while not telling Yoshida to do everything over again ("redesign all characters"). You can start them all from fresh and I'd like that too, but I feel that would require more work and even work into the armory system. While this grid system would take a new UI element you wouldn't have to redesign the classes, just bits and pieces / reorganization of the jobs.
If all skills changed it would help out logically, because only some changing would be a logical inconsistency that would look like the dev didnt polish the game. But then how would you make the white mage adopt cure without changing it?
I suppose you could make the Jobs their own but only take 5 skills from classes (so the ratio is flipped).
Also this grid/cryst/sphere system lets Jobs level on their own - making the duo jobs from class system possible for two reasons 1 jobs can be their own 2 jobs are further their own as they level on their own