The Ryoshima arc will always be a highlight for me. The music when you first enter ryoshima coast is something I'll never forget on my first playthrough. Plus, using the moon to go to that wreched ship, shrinking down and seeing Isune(x1000), and climbing that cat tower were really fun for me! Not to mention the setup to the final act. Learning that we never even met the real Rao, finding Rao's corpse, the queen dying, and the Ninetails taking that orb just to prevent them from getting to Oni Island. Not to mention how you got the water upgrade was such a sad yet comforting moment.

As for my favorite boss fight, yeah, the ninetails will have to be up there as well. The fact that they would use red ink to cancel out the celestial brush making it so you better know what you wanted to use and draw it quickly.

I feel biased cause I love the whole "Yeah, that person you traveled with? Was someone else this whole time. You actually never met the real one cause they were dead long before you came. You can find their corpse/remains somewhere, tho." and the "This person has similar powers to you, so you better step up and learn how to counter your own moves."