I'd like to see a lot of things. A few off the top of my head.

-Ability to mail anyone in your FC (or just anyone, the RMT thing doesn't happen in other games)
-Ingame personal parser (debatable I know, personal preference)
-Crafting from retainers inventory (make it so you need to be beside the bell if necessary)
-FC event calender. Seriously, why isn't this a thing?
-If you own a pet/mount/card, it will have an "already obtained" tag in your bags.
-Cards/minions on a personal loot system in alliance raids.
-Fully revamped Mount/Minion guide, larger window with an image of the mount/minion, search bar, verminion stats and so on. Collecting is a big part of the game, make it more attactive to view your collection.
-On that note, achievements with minion/mount rewards for collection breakpoints (such as "collect 20, 30, 50, 80, 100). TT does this. Make collecting a real, desirable goal.
-Flexible raid sizes. This would take development but would be well worth it and greatly encourage FC activity. Fine if it's not for Ultimate, due to balance.
-S Rank spawn alerts. Something like "you hear a mighty roar" when you spawn one.