Besides just having more room to hold stuff, I would like to see storage consolidated into simple categories. Instead of having the safe, locker, satchel, storage, and bag, and have all your items spread throughout, could you not just have one spot with more room?
I would also like it if you could auto arrange items by a category, like move all weapons to the top, or headpieces, etc. Or have weapons and armors in a separate box.
Lastly, Armor sets. It would be nice if you could make a 'set' of armor that you could quickly pullout of your storage, sort of like in the Monster hunter games, if you haven't played them, they allow you to register armor sets that you would use for different situations, and you can just go to your box, select a set, and poof, it's equipped...
Mostly I would just like to spend less time searching through all my items to equip myself when I want to change jobs.