I know that FFxi is far from perfect, but far as I'm concerned, its actually has substance that modern MMOs do not. There are two things that I want to discuss which frustrate me about the game to no end. The massive number of QoL NPCs, and the UI controls.
By QoL NPCs I mean the sparks and accolade NPCs, voidwatch, the various moogles, etc. It great we have all these features and I'm not complaining about them. What irks me is that for every NPC that's added to the towns, the more cluttered up the world becomes. Some NPCs have been added organically like the ones that bundle arrows and ninja tools in the circus tent that appears in the nation highest in conquest. But most of them, just stand out like a sore thumb... I see Voidwatch NPCs everywhere, moogles, moogles, and more moogles (don't get me wrong, I like moogles), the sparkle NPCs are right in the way, and everything associated with it has you deal with a clunky menu. It would be best if we consolidated all the NPCs in one area, that functions a lot like an the inns in FF14, so they don't constantly break the immersion. We can have a place like the chocobo arena and call it Moogle World and it can have a tutorial area and everything.
The second thing I'd change and it's a big one. The controls. Here's what I mean: the ALT and CNTL macro palate sometime takes more than 2 seconds to come up, when I click attack it takes five seconds to draw a weapon, when I TAB/F8 it won't are target a mob in front of me it will target something/someone like a mob in the distance, or a trust NPC I cannot have meaningful interactions with, etc. etc. all of this means when I want to target something and use an ability I want to go BANG, it takes forever. Also, who's idea was it to remove the ability to target F1-F6 your party member while auto-attacking? I want to use the <t> function to heal people which works instantly, not use <stpc> which requires an extra step.