To be honest I think that they way they have made the class system was a mistake from the beginning and was the remnant of the original plan that was removed before launch.

The original idea was to let Physical Level dictate your Job as it were, it being a blank slate completely devoid of any skills and abilities. Then you would build a job by unlocking skills and abilities through mastery of weapons and build a custom job of your own and distribute stats as you saw fit to build a completely unique character the way your saw fit. They switched it around though and made Class Rank dominant. This has thrown everything out of whack as it has essentially made Classes Jobs but because they weren't designed to be Jobs it has just created a mess of the system and everything lacks definition as they were designed to help you build your own custom class. Though you can still cross class things it has been scaled back from it's original design and this is why it is all a bit meh.

For me I would love it if they just did away with the weapon=class system, I want Job's that define themselves and that can use a variety of weapons. So if I am a PLD I can use a G. Sword or a Sword and Shield, if I am a SAM I can use a G.Katana or Polearm. I want the freedom to use different weapons for different situations but depending on the Job would depend on how skilled I am with that weapon. FFXI did this very well, it allowed you to use multiple weapons and depending on the Job they would cap at different ranks so some would be better choices than others.

Of course along with this they should definitely lock weapon skills to the weapon to help make them unique, this would also help with animations as they wouldn't have to model every single weapon skill for every single weapon.

You can see SE are trying to move in this direction with the implementation of Job's to define the classes but now they just need to go that extra bit and make the classes stand on their own. With the removal of the Physical Leve we may see this as what will happen with EXP. EXP would be used for your Class Rank, so for example a MRD would gain all it's skills and abilities as it levelled up from EXP minus the weapon skills and then the weapon you wield would level up on SP unlocking Weapon Skills and your proficiency with the weapon.

Most likely that will not happen but damn I wish they would just do it, it feels like the way they are approaching it is to just stick a plaster over the issue.