Biggest being the market wards and the current repair system.
Honorable mentions:
• Uninspired and giant unvarying landscapes.
• Identical camps.
• Levequests.
• The action bar vanishing between enemies.
• No mail system.
• No Linkshell controls and the ones we have require being on top of the person to be functioning.
• Most spells are just different color explosions and the casting animations all look identical.
• Terrain annoyances.
• Unnecessary clicks to use UI.
• Inability to use the mouse exclusively to run or at least the option to map it.
• Some races still only have 4 hairstyle options at the moment.
• Stopping to draw or put my weapon away.
Those are the things that annoy me. There is other stuff like a lack of chocobos and airships but I do not require them.