Like Axle said, Sky Keep provided some challenge beyond the regular SS dungeon. Major headscratcher, and even though I absolutely hate and would never want another Sky Keep-type dungeon to return, they're definitely a worthy challenge. Most of SS' dungeons I felt were just too...small, I guess. We didn't see enough of the underworld of Ancient Cistern IMO, most dungeons didn't have more than two floors. I dunno. They're good dungeons, but I didn't like their difficulty level.
I don't believe that SS' bosses are the easiest healthwise (honour reserved for TWW and TP), however by strategy I personally found that they're about as easy as Twilight Princess' bosses – biggest difference being we don't usually find a weakspot in SS bosses and we just wave our sword around like fools. I mean, compare Diababa to Ghirahim. With Dia, we have to first bomb him THEN attack his crazily weak weakspot. Ghirahim, we just have to lead him on [that's kinda creepy thinking about it] then we can attack like crazy. To most, Ghirahim would be the harder boss and rightfully so – we've never as far as I know had a boss like him (though Iron Knuckles from AoL were sort of like him).
Bosses throughout the Zelda series, not just SS, could use multiple phases that go beyond 1 on 1 fighting though. That's another factor – despite the size of any boss, we still only fight that boss and that boss only (with the exception of, say, Twinrova).