Skyward Sword has my favorite set of dungeons in the series with Twilight Princess coming in second. I don't think there was a bad dungeon in SS but I do think the first two, especially Earth Temple was quite short and could have been made longer. Also there was some redundancy. Why two fire dungeons? Also why two desert dungeons with timeshift stones? Although these two were different enough- Mining Facility vs Sandship.

I also think Twilight Princess had some very good dungeons. I remember not liking Lakebed Temple the first playthrough because it was so confusing but now I enjoy it. The only one I still dread doing after 4 playthroughs is City in the Sky. Something about the design makes it more drawn out and tedious than it needs to be.