It persists because it works. I've played WoW from classic to MoP. Back then, you had 10 different ranks of the same ability that'd you go back to your trainer to learn. A lot of them were nigh useless and just inflating your skill set.
Hunters had melee skills when they're supposed to be ranged. It doesn't even help that their melee dps is utter garbage, comparable to that of casters. Warlocks had "Detect invisibility" which had no PvE and PvP function. Literally because stealth =/= invisibility in that game. Mages had an ability that would display buffs on the target. Warriors had an ability that worked as a taunt...which is only usable outside of tanking stance (mind you any warrior, regardless of their spec, can use a tanking stance) the list goes on.
There were also a lot of other skills too; and you know what? FFXIV already suffers this to some degree. There were skills that worked as mediocre DoTs, debuffs, or provide yourself with extra evade as a dps. No one ever used these in an actual raiding environment because it's a waste of GCD and class resources for very very little benefit. We're seeing that right now with feint on DRGs and RoD for BRDs (only saving grace is that it can be free from wide volley, which is another problem of its own). Freeze immediately becomes irrelevant, cover has very little use unless the tank (me) isn't doing my job properly. Heck, most MNKs opt out of using fracture even when they have TP to support it to an extent because it's still a waste of a GCD and uses far too much TP for it's damage.
You said WoW is damaging the genre for what, being a success or setting the trend? What about other games that are doing the same or have done the same before? A lot of platformers are tacks of the mario formula; you can only add so much without changing the inherent design of it. It's working for a reason, and a lot of the things you're trying to suggest are also the reasons why a lot of rising MMOs have falled out.
And to add on, crafting does feel like another environment of it's own, since you can gear it up and everything. However, it has its own issues going on right now with the heavy emphasis on RNG. Some people also feel that that the classes are too similar to each other, though that's more on how the mechanics of crafting were designed to begin with. I don't really see this as a problem; but making each of the DoH classes unique to each other requires redoing the entire mechanic. I would love to see them step away from RNG crafting for end game for a bit, especially since it involves RNG and time gated materials.
And because that they're the backbone, some jobs don't deviate enough to add onto what they can already do; they feel like another gate to just learning new abilities. But it's also because that the jobs add abilities to a class makes it also unfeasible to go in as a class for the most part, especially as a archer who gets almost no benefits from having a variety of cross skills.
You could take away the jobs for each class, and they'd still play the same because of the baseline that is the class. It's also because of this that you can't really introduce two jobs to a class to have different playstyles if they'er within the same roles (such as Thief vs Ninja that was brought up a while back), unless you add in some sort of polarizing ability that drastically changes their playstyle, a weak example being defiance.
Having an element wheel creates class segregation when it comes to progression. Without redoing the current mechanic entirely, how do you expect a BLM to dps if the mob is completely immune to ice or fire? Or let's take away that mechanic, now suddenly BLM becomes a typical single-target caster dps. Or by some weird chance, they're fun to play. If they can do extra damage by just spamming fire (which may or may not be fun for some people), why would we bring a SMN or any other dps that cannot captilize on that weakness? Unless a BLM exploiting an element weakness does the same damage as a DRG would normally...now why would we bring a BLM on boss encounters that do not have elements applied to it?