I want to vouch for it's strange plot progression and world layout while still maintaining Zelda-style action, exploration, and dungeons.
Actually, could you be more specific on this? (Having not played it yet and all...) Isn't this what the Zelda series does anyway? It maintains "Zelda-style action, exploration, and dungeons" (because it's Zelda, obviously), and the main focus is on the changes in story and environment...On top of that you have new gameplay mechanics added through new tools for Link to pillage and use...
In Okami, there are a few dungeons, but they are not "goals" by any means. There is a series of mysteries in the plot (similar to the first half of Twilight Princess) but the goal you must accomplish is sometimes just go to a town and talk to a bunch of people, or do some random task in a town you've already been to. It's not nearly as "rigid" as the dungeon-hopping in Zelda, where the game is clearly 8 dungeons strung together. Again, I want to offer the first half of Twilight Princess as the antithesis of the second half. In between each of the first three dungeons were some amazing things to do, like the warthog battles and such. The game felt alive, even though there were dungeons. As soon as I got wolf form and the game told me I had X number of dungeons to go, it was all over. The stuff in between became optional.
In Okami, the lead character Amaterasu does gain "new abilities" with which to fight a few bosses, but sometimes these new abilities help her with other functions of gameplay and are much more important to progressing through the world than they are to fighting. The fighting system is more RPG-like, where you must whittle your opponent down with A LOT of attacks, rather than the puzzle-style bosses of Zelda.
In Okami, the plot drives the action. The overworld is not a circle with dungeons peppered on it, but a connected series of environments, forests and lakes and beaches and deserts and hills, in what honestly feels like the old 2-D Zeldas made 3-D. When it comes to dungeons, Okami could care less. It's much more about the unfolding story being revealed in cities, in forests, in conversations, and yes, in dungeons too. It's just different in a way that I love.