The only downside i see in having Classes and jobs and every expanding lists of them plus their skills is the same problem Guild wars 1 ran into. Balancing X skill from one group to X skill from another can sometimes be hard to balance across a spectrum of many many skills. So far FF14 seems to have done a good job of this on the surface. But at times you can see the conflict.

Few run anything without the protect spell when leveling. To counter that your average lets say, Battleleve must be tuned to take this into account. Skills with TP use are probably tuned with Invigorate in mind. since most anyone whom uses a class with TP use loads Invigorate.

I like the Class and job system alot myself. I like having a relative swiss army knife with the class i want to play. and the specialization of the JOB system for when i need it. What always worries me with any game that loads up on skills that can be used by many classes is that your skills available will be watered down and generally unable to have great effects due to cross class skill use.

But i should propose some sort of solution. Though its one i'm not generally fond of i think SE's new GC "Enchantment" system comming for patch 1.22 is a good step. And that is keeping very base effects on the skills and adding and augmenting the power and effects of those skills on the gear only that class can use.

Personally i'd rather have them as an addition to whatever armor you choose (Especially since i also greatly support things like appearance tabs and customizable appearance) That way they can tune skill bonuses to the class meant to have them while still keeping cross class and base class skills relevant.

Despite my concerns over watered down skills or broken comination of skills i fully support Classes AND jobs co-existing and flourishing.