1) Restore the Armoury System to like it was at the end of 1.0 as a base class with 1 Job crystal attached as an upgrade which would bring consistency to it, (in other words, give classes to the Heavensward Jobs, such as Musketeer (MSK) for MCH, Ravager (RVG) for DRK and Mystic (MYS) for Astrologian, and separate SCH from ACN and give it a new base class like Mediator (MED), and stop tinkering around it's edges.
2) Make a slight change to FATEs like Campaign Battles in FFXI in that to participate you no longer just have to move into range of the FATE, instead you have to click on a FATE status button that will allow you to participate, as FATEs as they are are very distracting when you don't want to do them and have to pass through one in order to get where you are going! This would also make quests/leves easier which happen to use a the same spot a FATE has spawned in.
3) This is probably more unlikely now given 3.4 will add the GC Platoons, but I would still love to see 1.0's Path Companions return as an alternative to the Companion Chocobo.
4) It's more of a minor thing but the weather changing being tied to certain times on the clock is stupid and not realistic at all - a more random weather system would make things more realistic, as I can literally watch to clock when it's raining to know when to expect it to stop.
5) No more non-FF related crossovers events! I know plenty of people who hated the Yokai-Watch event simply because it had absolutely nothing to do with FF and seemed like a a waste of time (and if that was bad enough the event had all the grind of the maligned atma part of the relic weapon quest). I like the crossover events, but the Yokai-Watch event took things too far. Please keep the crossover events to FF games as they at least make a little sense to be included.
That's about all I can think of at the moment.