Alright, I'm revisiting this thread to tell y'all why Ikana is the best.
First, we have the history.
Ikana, like few other places in Zelda lore, is dripping with history. As you interact with the places and events in MM, all to access the Stone Tower Temple, you find yourself thrown headfirst into a war between the loyal servants of Ikana and the strange and mysterious ninja Garo. Even more intriguing is the fact that this hatred and war is so intense that it is still being fought centuries after those involved have died. The spirits of the two peoples still carry on the war to the present day. That alone makes it an fascinating and harrowing tale.
That beings us to the atmosphere.
As you walk through the ruined kingdom/village you really sense the loneliness and desolation of the area. A place that is cursed with war and blood. You can feel it hanging over the entire place. MM and OoT mastered the art of creating atmosphere better than any other Zelda game imo, and Ikana is a shining example of that. I love hauntings, I love halloween and scary stories and locations. Ikana has all that, but not in a cheesy way either.
The creatures that walk the land, the walking dead and the Garo, tell you the story of the land. Often in cryptic terms, but that adds to the atmosphere. Another thing I love it history, and as you walk through Ikana you can feel the history.
Stuff to do
You have the Stone Tower Temple as well as the Ikana Castle and the Well. You have the music house in the middle with the little girl and her father you have to save, in doing so creates one of the greatest/sweetest moments in Zelda gaming. You can fight the Poe sisters and come across any number of odd and strange things in Ikana.
Lets not also forget how the Stone Tower Temple, with all it's odd symbolism and references, is one of the enduring mysteries in Zelda. Namely, being the only place in MM, an other alternate dimension from Hyrule, to depict the Triforce. Also don't forget the strange and mysterious Mirror Shield. As a kid it gave me nightmares! It's as if some trapped spirit inside is crying out for help. To add to the creepiness, the Happy Mask Salesmen has a mask identical to the face on the shield.
It makes you wonder, what connection could the HMS salesmen have to Ikana? Or maybe the question should be what connection does Ikana have with the HMS and Hyrule?
Either way Ikana is easily my favorite.