My impression of all this is that yes it was kind of a ham-handed ending, but then, what's the alternative? Another one of those, like the lying pancreas in cooking April? So yeah, I'll take the ending but I'm much more focused on the journey.
The sciencey mumbo jumbo ended up being distracting as well as a pain in the zit-infested arse to translate, more so because it didn't really make any sense. It licked the surface of some of the scientific theories so i wanted to make at least the terminology consistent. It's been many years since my physics classes and I've retained pretty much nothing from my engineering school days.
But once we free ourselves from the need to actually make sense and start to speculate wildly, the story does become more interesting. I particularly like the part where Kouji apparently gives up control over his reality and merges into Tokine's. That has an implication with regard to the ending where they may be in a perpetual loss time of just those two where whatever they wish is granted, having been freed from the shared perception that are forced upon us as well as are dependent of us.
Or it could be a standard happy ending where Kouji becomes a doctor and invents something that makes Tokine wake up and they make wild love and have like 10 puppies.