After seeing this in the news, I decided to revisit it. I beat it back around Christmas of 2015. Some enhancements I would suggest / hope they would address.
Nitpicks:
Remove the animation where Link picks up an item and you see where it is in the inventory upon every new play session.
When dropping to the surface, show the actual map where each bird statue is, because I rarely remember the specific spot without seeing the map. The painting is pretty, but it would be nice to be able to zoom into it.
Add the ability to go from area on the surface to another area without having to jump from.
There aren't that many quests, but a small quest log would be handy.
Options to filter how much Fi talks with Link about gameplay content vs. story content
Content changes:
(These change the fundamental game and may work better in a direct sequel so they might not even be worth mentioning but ah well)
Button controls. I don't know how they'd do it for combat, but a lot of things like flying, swimming, using the beetle or really any of the items, would be great. I speak for accessibility more than anything. Let's Go Pikachu & Eevee having required motion controls when docked was very disappointing to read about. Wii MotionPlus worked great, albeit not perfectly. It still works great. But the option would be great.
More content in the Sky. Add some puffy clouds for Link to shwoomp through, or some weather effects, or rainbows, or lightening you have to avoid. Maybe a few islands that the Skyloft people haven't cultivated yet that you can explore and find specific crafting materials and / or insects. Maybe there are some characters like the Rito who also live in the sky that you can find later in the game like in a segmented area. Or maybe it's just a few and they are endangered and you have to bring them crafting items to help rebuild their home like with Tarrey Town. Lots and lots of ideas here. But more than anything....
Let me fly at night
Make all three segments of learning the Goddess Song (that notorious padding after the Fire Sanctuary) optional. That part really kills the enjoyment. You'd have to rework / change the pacing of the story a bit.
Very new content that I don't expect but hey it'd be cool:
Groose Tower Defense side game?
Impa / Zelda side mode where you get to experience Zelda's experience on the surface running from Ghirahim rather then watching it in the credits.
Configure all three Imprisoned fights into one fight were each stage has the Imprisoned change.
Add some upgrade options to the Stamina Meter...this could maybe tie into some of my ideas on beefing up the Sk