I actually don't know how to answer to thi thread. The thing is I actually liked all dungeons and it is very hard to define a least favourite. I definetly don't hate any. But I do think the Lanayru Mining Facility could have been less tedious in some parts, blowing the Gust Bellows in the fans of the moving platformrms was kind of difficult at times. And I do find somethings could be better in other dungeons but nothing in itself flawed to say I do not like them.
And as to Sky Keep, who says there is no boss in that dungeon? Dreadfuse is a boss and is complex and hard enough to be considering as one. Ok, I know it does not have the subtitles, but consider how hard and challenging he can be. That guy pushed me to my limit and was harder than some bosses. So even if he is not technically the Boss, he is an enemy that can be considered a significant threat. And he is amazingly cool and badass. Definetly one of the game's most memorable boss encounters.
Also, why does the Sandship get so much hate? Sure is not the hardest dungeon, but I love the concept, Scervo is an amazing mini-boss and the item is my favourite along side the beetle. Also consider how clever some of those puzzles are, the way to get to te dungeon is quite creative too. It also helps Skipper is one of my favourite characters. And the view is utterly gorgeous. The water and sky painting rendered in the background is jaw dropping and was one of the best scenaries the game has.