I hated The Imprisoned. The music was obnoxious, and he looked like Barney's evil twin.
I would say my least favorite temple was the first(hated the music, felt powerless) aside from one tiny thing: the Beetle. I loved the Beetle, the ability to use it and upgrade it, making it both a powerful tool and an excellent scout, made the first temple bearable.
The Mining Facility, on the other hand, infuriated me. The dungeon itself wasn't too bad; that wasn't the problem. The problem was the dungeon item. I had seen all of the Clawshot ports in the desert surrounding it, so I was SO excited about finding it inside the dungeon. But I opened the box and found.. The Gust Bellows? Say whatever you want, but that thing is nothing more than a magical leaf blower. Most pointless dungeon item ever. It's not even neccessary to beat the boss, you could just wait for Moldarch to pop up and try to attack you rather than chasing it with the stupid leaf blower.