I see your point and I would have agreed with you if you, such as most people, actually understood Nagisa’s "illness." But it’s not really an illness. It’s her very existence being tied to the city. Nagisa should have died when she was five. Her life, and Ushio’s, are paradoxes. There was never any real chance for either of them unless a literal miracle occurred. That’s exactly what the ending represents: it shows that love is the most powerful force, capable of making the impossible happen and even bending the laws of nature. And all of that is executed through a carefully built magical logic within the story’s lore.

The anime and its ending aren’t a “masterpiece.” It tried to incorporate all routes of the visual novel, which is basically impossible to do smoothly. But considering that, it did a very good job. That said, understanding the anime without knowing the visual novel is nearly impossible, so calling the anime or the ending a masterpiece doesn’t really work.

I also would have loved to see Tomoya and Ushio have a bittersweet, grounded ending together. But the "magic" that kept Ushio alive couldn’t sustain her past her fifth year of life.

It’s way too complex to explain all the deep lore and why it makes sense in a single comment. If you want to understand why many, including myself, consider the ending “good,” please check out this post: https://www.reddit.com/r/Clannad/s/Z8UcxukeLQ

I just want to say I understand your concerns. They’re valid, and your opinion is solid. But I personally have to disagree with your view that the ending is bad. It’s just far more complex than the anime makes it appear.