My "imo":
Glamour log - in comparison to major competition it is quite feature lacking
Housing - A point of contention that shouldn't exist, even if you consider the ward system as a good thing (say like LotR Online's ward which auto grow and shrink based on demand). Which to be salty lol- I don't think the ward system is a good system, the cost of creativity/development opportunity vs very few people getting to see a random house put up- not even remotely of worth and technically there are potential neighborhood systems that could function in a more personal world driven space too (or other systems that could encourage strangers interacting together), so not exclusive concept to wards. I think wards makes more sense when you go hardercore games, or even sandbox- not for a themepark though.
Inventory Management - Retainers, saddle bag, inventory- it could be a lot easier to manage all the items. Now this is not really an issue that plagues just FFXIV, but here and there it could be made easier to deal with. Also inventory management would be some of the annoying steps required to figure out if you've learned or own a certain content piece (like minons, music, or mounts- the three Ms lol).
Smoothing of combat - I don't really want to label, or think I'm confident enough to say what exactly is the issue where, but say for example the dancer dash skill- from experience with other games and then that skill I feel "this should be smoother and flow better". Now of course if you compare dancer to other jobs that can't dash like that then of course Dancer still feels with a movement in comparison, but something to do with the animation, code, steps in the ability, something, it's not too uncommon to feel like the system is "thinking" rather than just being a dynamic action. More pronounced examples would be fumbles with benediction or hallowed ground. What your brain thinks it should be, at least imo, is not always what happens. It's not insufferable but occasionally notice-able enough to be like "is that a 1.0 remnant?" lol. Something something the system needs WD40 lol. The glide is missing.
Fantasy Role Play - no not Balmung Role Play. I mean some jobs I feel could have a lot more 'character' about them. Something that paints the job more to it's story / style. Dragoons being able to jump higher, or at least get a special mount unique to them (better yet if it was an ability, so it had special rules). I like to example WoW for this since it's something they clearly went out of there way for, first example everyone will see when playing is the race role play aspect. Now I'm not suggesting racial abilities for FFXIV lol, but how you see certain races and certain jobs have special functions due to what / who they are. It adds a lot of the vibe. Like if you're a Demon Hunter so you've got wings and can glide about, you're constantly being reminded that eyy you're a demon hunter and you've got WINGs. Abilities help sure, I'm not saying all the jobs are the same, but I feel there is a lot of room for SE to improve the 'story' of their jobs via this type of content. This content I think would also be a bit smoother in FFXIV since we've a job system. This role play can and should carry to things outside of just the jobs. For example your chocobo might grant you access to special areas, or if you're a dragoon you could follow that path too, such that people exploring a zone might find a hidden grotto with a treasure or something. For crafting jobs like Engineer in WoW there could be some cool toys, everything doesn't have to be so straight forward and to a template.
Gear - I feel gear is extremely transparent now as a ladder rung that they don't even need to have gear anymore. Stats are on your character and you level up your character by doing content. Finish a dungeon, +ilvl, once you finish it too many times you can't gain power from it anymore- do some other new content, when SE wants catch up patches they just make older content award more and take less runs. Now that is leaning into the simplification obviously, such that gear is literally just glamour then, but we could of course go the other way and make gear have some character (fantasy role play again). Such that the epic jumping boots of leaping lizzy would you know.. make you jump better.. lol. More interesting effects. Also just wanted to pass a shower thought I had that I find how gear works currently is counter to how a single player game would make difficulty work- such that skilled players getting better gear makes the game easier, and I think there might be something interesting in going like- the harder to get gear makes content faster (by more damage) but makes content also less forgiving (you'll take more damage), as such casual and or lower skilled players are likely to complete content and see the fight's entire offering while skilled players need to play even better but will complete the content faster. This in effect creates minor horizontal progression, and due to the difference may also allow room for special effects. Relics and crafting gear can also then take up a place that is more defined between that point. Such that all the gear of a particular 'rung' on the ladder share the same ilvl but their distribution will be different for different styles. The ratio to defense and damage gain should be a bit aggressive though, if it was equal then it would be really easy to choose the offensive gear. No I think it should be more thought than that. And such people who are doing brand new savage/ex/ultimate might try it in progression gear first to see as much as possible, and then try to carefully witch some pieces to the offensive pieces. If they went all offensive then they'd have to play near perfect. Savage / ex content wouldn't be released to DF until the progression gear was strong enough to reasonably break dps checks (so maybe when SE wants to add echo lol). Either way I still feel like SE is in a weird place where gear is just a formality, they could easily do away with the stats on gear and make the system smoother for everyone (just glamour), or get creative and bring some heart into the gear.
This one is a hyper imo, not sure I'd argue it as a core plague issue just I feel something I hope they're tossing ideas around-
Long term progression (that I'm going to infuse with 'role play' issue above)- I keep thinking that there could be a lot of interesting and decent nostalgia hit for some players if they added a sort of cosmetic / role play merit system. In the style of a license board or sphere grid. Here you would unlock a slew of job and general concepts keeping value of exp past once you hit cap. This could also add some nice flairs of value on content too, like the FATEs with exp bonuses could grant you merit exp even though you're not capped (as an extra treat and it means players can have this system with them for a long time, from the beginning to the end). Of course different items would have different costs, and the system wouldn't be 1:1 exp value (so that way the math doesn't become really wild and weird as you go from level 1 to level 80). Some sort of consistent conversion calculation. You could have a lot of cool cosmetics like unlocking the heavensward dark knight shadow effect for your aura, changing abilities looks, special job mounts for the jobs that didn't get a chance before (big cost of course), unique gear especially neat if the gear breaks normal concepts so like White Mage might be able to earn that sort of FFXI holy breastplate look (battle cleric vibe), but also onto role play. So for example you might have certain mages learn job specific teleports, and you could even add a tier to the ability where you can teleport to location as that job but if you upgrade it you can use it as any job (adding QoL but also obviously makes the merit system last a long time as skills have levels too). Dragoon would unlock no fall damage passive, enhanced passive jumping, special jump transportation mode. Bard could 'purchase' how to play certain instruments. An expensive bard mount might be in a comfortable sitting / playing position and the music from their instrument holds them aloft (better yet if this special mount can actually play a song they save or something like that, or let them play to other players while moving). Dancer with new choreography dance system / emotes. General purchases can be made too of course, like perhaps a hyper expensive one would by the flying 'mount' like you see when you're in cutscenes with mother crystal.
Because of the progression concept and opportunities to earn it, sometimes, not at cap you could have some cheaper ones that are easier to obtain- such that dragoon player would be able to learn half fall damage at like level 30 almost right away, and no fall damage at like 45-50. And improved passive jump (like they can hold the bar to charge up and leap higher / with great forward momentum if they're moving) at like level 60. Yet of course there would be upgrades and certain paths that would be the sort of thing you'd be at cap for a long while and be purchasing. Like you might be able to unlock a special teleport (like Altep / portals in FFXI / WoW) as a mage pretty early on without too much pain, but in order to unlock that teleport to be used when you're not that job it would cost a lot.
To be fair there are a lot of ways to do long term progression though. Like I'd hope for airship content being something like that, or chocobo. Or you might come up with some other concept. I just think leveling is loads of fun but once you're out of leveling one of your main long term progressions is on hold while you do steps on the ladder for gear which isn't quite the same type of progression since that one slides a bit (gear undervalues gear, since we're linear based which is fine but it is what it is).