I would love for them to revisit older parts of the game.

Chocobo
Bring it up to date, like removing outdated stats like accuracy, and give it more/better things to do.

An interesting overworld
The ARR overworld is really interesting, but the further down the expansion lines we go, the more empty the open world becomes. Side quests help a little, same with fate. But side quests you only do once, and fates are so easily stomped on because syncing is completely screwed up in this game (Bozja skirmishes melting like ice for example)
I think flying ruins a lot of the game, and that we gain it way too easily. I'm not saying it should be as difficult to unlock as it can be in MMOs like WoW, but just a little more.
Mindblowing to me that it took them until ShB, to realise that maybe they should give players the opportunity to gain mount speed increase earlier than AFTER completing MSQ.

After we got flying in ARR, I really wished they would add something to the areas we suddenly had access to. So many empty high up areas that just screams "we were not intended to be seen!"

An world that changes over time
With the moogle tribe, you help them rebuild... a square, rest of the zone is perpetually still in ruins. Wish that over a long time period, maybe sped up by helping them, you could see the moogles improve more in the zone.
Same with Ishgard, The Doman Enclave (what wasted potential) Garlemald, and for that matter, Gyr Abania! If nothing else, an airship landing in the Lochs. So that you can travel from New Gridania and to the Lochs with an airship.

Island Sanctuary
Making it a cooperative experience would be so much better.

Gearing should be more flexible and interesting
The substats are boring. Tenacity feels pointless, Piety is "take only as much as you need".
Speed is generally only a "take a little to reach a slightly better speed for comfort".
Beyond that it is mostly just a rule of "as much crit as possible, then DET/DH."

For a game about playing any job you want, they really hamstring you when it comes to raiding gear, to an honestly baffling point. Only one piece per week, and that even applies to alliance raid gear that is near pointless for anything other than catch-up and fashion. If you are unlucky, you could be spending months of clearing just to get 1 body/leg piece. That's insane, and a fast way to burnout.

Grand Company
Keep them relevant throughout the game. You keep feeding them items blessed by gods, yet the best they can trade you is a coat for level 50?
Beyond pvp, there should be more reasons to care about the GC.
Ishgard as a Grand Company should be possible.
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I could probably go on, but yeah....