Some needed gameplay improvements:
-Have a menu to select party members. No more of this "find them in the city" bullshit
-Have dormant party members scale levels with the main character. This game has like 20 party members and you have to level up each and every single one of them. Ain't nobody got time for that!
-Let me accept more than 20 missions at once.
-Increase the font size
-Give the option to play the regular continent music while flying in the Skell.
-Give the option to lower the volume in the cutscenes.
-Replace the soundtrack with Xenoblade Chronicles' soundtrack
-You can cut down the requirements for the collectible missions too. Instead of needing 10 of an ultra rare item, let me collect 5. No one will miss those.
I'd ask for improvements regarding story structure, but that would probably require changing the game entirely.