Changes I would make:
No longer loosing of rubies, dungeon and quest related items going back through time.
Freeze the clock while in dungeons and/or outside of the main town hub.
Saving anywhere w/o going back in time.
Song of time, changed to give you an option of how far in time you want to travel. The options would be 3, 6 9 and 12 hours with an choice of forward or backwards. As well as a choice to return to the first day instantly.
I would have to disagree with most of those.
You do not have to lose rupees if you bank them, likewise losing ammo and all that worked for me.
I might go a half or three quarter speed clock as a kind of easy mode, or maybe a kind of item/song/minigame/race to the next point upkeep type thing. Alternatively I can see having a free five minutes from the start of the return warp do OK.
Saving anywhere, if it is a portable game then maybe a handheld RPG port style thing with the one time hibernate save would be good to add. The statue save system did OK for me, at least as long as it does not replicate my expansion pack overheating and preventing the save statues from working.
I am not sure song of time going backwards, maybe a once per reset thing.
I can support calls to make progress a bit more obvious but most of those would make an already easy game a cakewalk.