Idk, my only complaint was the saving by only using the owl statues.
You had the 3 day duration but once you get your ocarina back from skull kid you can play the inverted song of time to make time go slower or play the other song to skip half a day so there is no waiting period.
Stray fairies weren't that bad; you have a dungeon that can be easy or very complex, and you have the great fairies mask to help you locate fairies in the room you're in. Is it hard? Probably to most players but not to me.
Yes there is 4 dungeons but you also have a lot of sidequests to do before reaching the dungeons or not related to the dungeons at all. I felt like that it made up for the lack of dungeons and bosses to fight; you got the Spider houses in the swamp and great bay. You got the bombers notebook. And you got all of the other events getting placed before entering the dungeon or starting it. It was a nice touch to the game, but I guess majority of players want to bash through a long dungeon that is more complex than anything else.
And I agree, that bank issue is very dumb. I hated the fact that you can only max out to 5,000 rupees. I wanted to add more to my bank but it can only add so much. I hope it gets improved in MM3D along with the saving. Those are my only complaints.