I personally feel like there should have been more enemies to fight. The bosses that we do fight are all very simplistic – even moreso than that of Twilight Princess' bosses. There are very little variety in field enemies, I can count some 7 enemies off the top of my head but they aren't even obstacles – three hits or so from the G Sword will destroy them, two hits if using the Longsword iirc. We could have had more sword wielding enemies too; Dark Link would've had a perfect entry into this game what with the motion gameplay.
On the topic of sky, the Sky was too empty, I'm almost sure that is the unanimous vote. Besides having more goddess cubes/chests, I'd like to have mini missions take place on Sky Islands and Island Masses. Like, say Skyloftian Rebecca was somehow swept away onto Island XYZ. XYZ is actually a minidungeon in itself – combat based or puzzle based, then at the end of that dungeon you find Rebecca safe and sound, get your usual Gratitude Crystal reward (from 1 to 10 Crystals depending on how fast you completed the dungeon perhaps?), then you could maybe take her back to Skyloft on your Loftwing but with a speed decrease due to carrying two people. Having those to be replayable and with increasing difficulty (even if having the True Best Blade enemies should have about 10x defense so they have to take many hits), that would make for enough in my mind to do. Oh, and of course SS doesn't have a gauntlet. One could argue that Boss Rush is a gauntlet and it is, but it isn't like that of Cave of Ordeals or Savage Labyrinth, which disappoints.
With Grooseland, I wish there were more than three areas to explore. We see the same areas all the time, and there is no Grooseland Field to connect the land which is so ridiculous. Many NPCs could've been added as well, Grooseland lacked NPCs for sure.