R=U is the kind of story twist that would be totally cool in a game set up for it thematically and narratively, which is probably why it gained so much traction in the first place.

It doesn't really fit into FFVIII that way though. The story would focus on entirely different things if it had that kind of dark twist to it. I do appreciate the creativity that went into it though and think it's really cool that it even exists as a theory =P