I see what you're saying, about the story and characters not being developed enough. Despite that, I still think it's one of the best movies I've seen. I can only imagine what the thing would've been like if a huge chunk of his budget wasn't cut. I actually enjoyed the fact that the story was undeveloped, it left it open to the viewer's interpretation of the rest of what's going on, especially what connects the present and future stories.
My idea after seeing it was Show content
that in the present Tom continued his research and eventually discovered eternal life, which he used on himself. Then he waited until technology was advanced enough, and then he took his futuristic bubble spaceship with the tree his wife is buried under and set off for Xibalba, the place the Mayans and Izzy believed souls go when they die. He waited hundreds of years and eventually set off through space to be with her. I saw it as kind of the ultimate love story, so the actual development of the story was less important to me than the concept.