1) Revamp the squadron system and give them the same AI as the Trusts. This should've been done when trusts were introduced.
2) Create a Trust version of Castrum/Prae and require that to be done before Duty Finder MSQ Roulette unlocks, and then allow for cutscenes to be skipped in MSQ Roulette.
3) Poetics Vendor in Mor Dhona should offer the poetics gear from every expansion, so an overleveled character that is still MSQ locked can dump their tomestones and avoid capping.
4) Increased XP for ARR dungeons.
5) As someone said, every job gets an AOE rotation at level 40. This would be a huge quality of life upgrade for running lower level content.
6) Any content that was basically ported from ARR (Toto Rak is a HUGE offender for this), as someone else said, should have their dead ends removed. While they are at it, spawn the final boss chest dead center. Ever notice it's off center? It's because in 1.0, multiple chests would spawn at the end based on conditions one finished the dungeon completing. Up to 4 chests spawned. Now the only one that does is the boss chest, but it kept it's position. It's an OCD nitpick, but it always makes my eyeball twitch.
7) Fate XP increase, Hunt log XP increase, Side Quest XP increase for all of ARR.
8) Do... something... with Cape Westwind. Turn it into a solo duty or something and retune it. The poor dude's had years of being wailed on and meme'ed.
9) I like the suggestion someone mentioned of making your highest level job's job questline a requirement for progressing in MSQ. With one additional add please. A simple pop up or NPC text reminder of "EQUIP YOUR SOUL CRYSTAL".
10) Expand the Smith's role training. Add in an additional category: Common Adventuring Mechanics. Show off stack markers, confuse arrows, tank busters, esuna'ing debuffs, etc. Really any fundamental mechanic that should be exposed to the player. Also, make the role training from the Smith mandatory before unlocking the duty finder. Should a player level skip, and has not completed these, they should have to complete these right at the initial start after their level skip.