#1 - Crafting and Gathering has so much potential and yet it does not feel rewarding.
It simply fuels itself. You craft and gather... to craft and gather better.
It does allow you to make some HQ gear for leveling, which is at best equivalent to what you get from duties, but it doesn't really matter because the game is easy.
The time you spend leveling has nothing to do with how hard it is to do quests, but how much time you spend moving around or watching cutscenes.
At some point Crafting becomes relevant outside of itself, but that's for a small percentage of the game.
This might not bother me if the mini-game for crafting wasn't so enjoyable and interactive, but it is, and precisely because of that, my expectations for the system are higher, and so is my disappointment.
WoW crafting doesn't add to your experience while leveling either, nor does it have a cool mini-game, but it flows easily into your playtime because it is not excessively time consuming or disruptive.
#2 - The Class/Job design, despite all the improvements over the expansions - and it did improve a lot - still feels on rails and homogenized.
I like how the Abilities can be used outside the GCD of the Weaponskills, especially with Dragoon Jumps, and I also enjoy having positional requirements on skills.
But even with that, the numbers, the (often lack of) interaction between abilities, it's all so similar that when you change between Jobs of the same role, you're mostly changing aesthetics. Sure there is like one or two mechanics that stands out in terms of gameplay, like the Ninja Mudras, but it all runs on the exact same canvas.
I found this homogenization acceptable during the closed beta for ARR, but as expansions went by it's just been grinding down my enjoyment...
#3 - You can't really stand out among others of the same Job, apart from knowing the encounter/Job mechanics better.
3.1 - There is no customization - this is connected to #2.
You once had some degree of (bad) customization, but it turned out everyone used the same stuff all the time so they removed the "mandatory" stuff from the cross skills and now you have inconsequential choices.
3.2 - The skill ceiling is VERY low - cycling through a long pre-ordered list of abilities isn't skill.
#4 - If everything tries to feel special, nothing feels special.
Every ability is so flashy, down to the most basic ones. And the most powerful abilities aren't necessarily the most impressive either.
#5 - Story keeps telling me I'm special, powerful and chosen, but I'm constantly helpless, useless or forced to lose and be shown mercy or saved in the nick of time just to show how powerful my new enemy is; and every other quest I'm told to deliver a package.
Same issue that Crafting has - if the game didn't try to sell me on the idea that I'm special and powerful, it wouldn't bother me.
WoW has inherited this same problem since WoD and it's been getting worse.
#6 - Game still has some ridiculous limitations.
Loading screens between adjacent zones on an MMO with today's technology, despite PS3 no longer being supported.
Au'Ra horns and face can't be customized separately due to "memory", despite PS3 no longer being supported.
#7 - Nostalgia milking
Materia, Limit Breaks - all a bad joke of the original...
Materia are just boring stat gems - why can't they at least be ways to modify your combat with interesting effects?
Limit Breaks could easily be the highlight of the game as a way to express your Class/Job, but instead are just this pre-determined mechanic where the only variable is who pushes the button.
I guess at least 4 expansions later my fist-fighting Monk no longer has sword limit breaks anymore...
But seriously, if they like nostalgia so much, why not use the stuff that has potential?
FF7 support materia, proper personal limit breaks with different levels, timed input (Tifa LB)
FF8 skill junction, interesting GF passives, more timed input (renzokuken/gunblade shot on hit)
FF9 traits, skills/traits learned from gear.
FF10 sphere grid, interesting gear effects, more timed input (overdrive)