I agree that Ultimecia's backstory and motivations are barely addressed at all, which is what created room for a lot of theorizing, myself included. While I don't find R=U compelling I think certainly that Rinoa and Ultimecia were intended as contrasts to each other.

My own pet theory is that Ultimecia was a member of a future version of SeeD and when it was discovered that she was the prophesized witch her friends turned on her, which would give her both motivation to conquer time and space and explain her burning hatred toward SeeD.