It was hard to pin down what exactly the intended message of the movie was. The clearest message seems to be the importance of letting go. Mahito needs to let go of his anger from his mother's death. The Master of the Tower needs to let go of his legacy by not taking an heir to keep his world going. Himi accepts going back to her time, the tradeoff of being a mother to Mahito is worth facing her eventual death.
And that's a fine message and all, but there was... a lot in this movie that seemed very extraneous to that point, or even kind of unnecessary and somewhat confusing. I get it's the nature of Miyazaki's world building that not everything should be explained, sometimes things are the way they are even if they seem strange to us. But then you have things like the little cute spirits that Kiriko was looking after. They ascend in the sky to become people... so these are like human souls, and this world is playing into the cycle of life and death. Except... that's not apparently right at all. The world is a construct of the GrandUncle, and not really a pre/afterlife, so... what's the deal with them baby spirits then? Was Kiriko just wrong about them becoming people? And if she's not, that raises A LOT of questions about what the world ending at the finale implies. You might be noticing I'm not using their proper names, and that's because after checking some reviews and the Wikipedia article for their names, I don't see them mentioned at all. They're just that completely irrelevant to the overall story.
The whole basis for the GrandUncle's plot feels really odd. Basically, a meteor fell from the sky, he built a tower around it, and it's actually a magical space rock that makes him god of his own pocket universe. And that's all the elaboration we get on the nature of his powers. But there are also rules to the world that he abides by, such as building the block tower to maintain the world, and that the delivery room Natsuko was in is a sacred place people aren't allowed to go into, but only the parakeets really seem to care about that. And speaking of, some character behavior just feels odd. Why did Natsuko become so hostile to Mahito in the delivery room? Was she speaking more plainly her insecurities of being thrust into the role of his new mother, lashing out in grief for her dead sister, or falling to some otherwise unspecified corruption in the world? Why does Himi have fire powers when none of the other time displaced people in that world have something similar? The movie establishes Himi is Natsuko's sister, but I don't think that quite clearly sets up that she is also Mahito's mother, until they say it to one another in their goodbyes like they knew the whole time. What exactly is the Heron? All the other birds seem to be just altered birds brought in from the real world, but the Heron exists apart from it, and almost acts like he's seen this kind of thing after the other world collapses.
Maybe I'll appreciate it more on a rewatch. And again, I did enjoy it, the animation and score are beautiful, it's just not going to be my favorite Ghibli movie, and I feel it could have used some more focus and polish as a story.