I had a similar reversal on Majora’s Mask. I didn’t think much of it for a while, but somewhere along the way, I realized it was actually amazing. What also helped was the 3DS remake coming out; I forget which review I read it in but someone, somewhere, pointed out that the major theme is forgiveness. That’s some good shit right there.
For that matter, same with DK64. I was so into it when it first came out that I got all collectibles, but I can’t ever imagine touching it or its literal thousands of collectibles ever again.
While I’ve got Zelda on the brain, I wasn’t all that into Wind Waker when it first came out. I got it early on, but it never clicked with me. I don’t think I got very far. Then, one day, I got over my weirdly hostile distaste for the sailing, and wouldn’t you know it, it’s actually really good!
I can’t think of anything else that properly applies, but I feel like Paper Mario Sticker Star deserves a (dis)honorable mention, because I can’t think of any other game where my opinion changed so radically within a single playthrough. I loved it all at the beginning, and I hated pretty much everything about it by the end.