Ah! This is like getting to the middle of a Pokemon game, where your party is just getting so big you have to decide which one's to leave behind and which one's to keep on training (and whether or not you really want to be "that guy" who uses a Kadabra with Psychic as his lead)! There are so many things to say about this!
Without a second thought, Okami takes the gold for world design. The game by itself is amazing - but when you pair it with knowledge behind how they designed even the most insignificant characters, or how the relationships between them are nudges towards countless Japanese myths and folktales, the game adopts a whole new level of depth. It takes time to look into the world of Okami, but it takes all of that Zelda charm and throws it into a blender alongside an extraordinarily deep understanding of Japanese culture as a whole - going so far as to remodel the entirety of the Japanese capital city and courtly life. I don't even need to mention the graphics, and Shinshu Field is arguably as iconic in feel as Hyrule Field from Zelda or Azalea Town in Pokemon - this game, though, stood on it's own (until Okamiden). In the Japanese version, Waka, whose named after a type of Japanese poem, speaks in the format of the poem of his namesake. That being said, the depth of design and attentiveness to charm, cultural material and overall aesthetics makes Okami my personal favorite in this regard, but...
My girlfriend and I woke up at midnight to hunt down Skyward Sword, which failed, and the next day we spent a good four or five hours searching for two copies of the collectors edition - which succeeded. Aside from that wonderful referent for the game, Skyward Sword did more for the franchise than it did for itself. When I played it, it truly felt like a 25 year culmination of all the things I loved about Zelda - from the whimsical charm of Batreaux to the epic score providing the back drop for the battle against Koloktos - it was a game that, to me, nudged Ocarina of Time out of it's throne. It seemed to me like Nintendo's first step in a very right direction without completely "modernizing" the name. It found it's graphical niche, despite some obvious flaws (Fi's singing...ugh...ack...), and combined a great value of nostalgia with new aspects of "modern" games. Like I said, it did more for the franchise and Nintendo than it did for itself.
This thread, it rips my heart in two!