Yeah, I thought the Deku Palace sequence was a great nod to OoT's Hyrule Castle Courtyards as well as the top-down gameplay of Zelda yore. And then there was the axel element of Z. Unlike the majority of the courtyard shenanigans in OoT, there was extensive use of verticality to navigate the gardens of the Deku Palace. I also found it conceptually interesting in that the Deku Palace is the first 'castle' you venture to in MM just as Hyrule Castle is the first in OoT, and yet it is run by Deku, not Hylians. Culturally different, structurally similar. An interesting take on the parallel world concept.
That's not to say Ikana's Ancient Castle isn't Hyrule Castle's Terminan counterpart though.
Edit: Despite my love for the dead culture of Ikana, I may find the Southern Swamp to be my undying love for Majora's Mask. As a child, I despised the region for its sheer alienation of all things comfortable and safe. There was layered danger around every corner, as one would expect to find in a swamp. Such an uncomfortable place to venture into, and yet that's basically the first part of the game. The desolation of Great Bay is unmatched by anything Zelda, even Twilight Princess. Something about the grandness of the ocean, the grainy boundaries of the murky water, and the horror of Like Likes populating the sea floor. I could go on, but Majora's Mask nailed atmosphere. It is terrifying to venture around Termina.
After Skyward Sword and an original 3DS Zelda, I want nothing more than a remake of Majora's Mask.