Thanks for doing this episode, at least I now know why other people love this movie. I think I'll have to watch it again, but I'm still not convinced it pays itself off for me.
My problem with the movie comes down to a lack of symmetry between the three stories. Any one of them is fine, but they don't add up together. Even if we narrow the story down to boy+girl, we've got a story where Tomas is following Isabelle's bidding, a story where Tommy is trying to save Izzie so hard that he's ignoring her, and a story where he's isolated while eating a tree that symbolizes Izzie. The central story is neither mirrored nor contrasted by the other two parts of the triptych. They seem mostly held together by actors, colour scheme, and a love of geometry.
I'm not clear if the future section was a metaphor or literal. I'd be fine with either, and love it if both options added up and made it ambiguous, but neither adds up. Either literal Tommy didn't learn anything by the end of his story and spends 500 more years in isolation and mourning, or it's a metaphor about him slowly killing Izzie by living off of her in order to reach enlightenment. The literal option is depressing and breaks the emotional arc of Tommy, and the metaphor isn't paralleled in either other story.
The inconsistency in the tree symbolism really frustrated me. In the future Tom is living off a tree. We establish that it's an Izzie-tree and that it keeps him alive for hundreds of years. In the present, there's the plant he studies with special properties AND a tree seed Izzie gives him that he eventually plans on her grave. It would add up so much better in my head if they were the same organism, but they're just not, for no apparent reason. As well, in the past, the tree is the Tree of Life. When Thomas finds it he ends up sprouting Grim Fandango style, becoming part of the tree (and the ciiiiirrrcllllle, the circle of life). So in the past Thomas becomes the tree, when we already established that the tree is Izzie, which is just kinda awkward.
In the end I felt like it was this close to looking gorgeous AND holding together, but just doesn't for me. The lack of internal consistency in a movie that I want to love just makes me go bleh.