Just saw Wicked two nights ago. I came out of the theater feeling like I could fly. Such a magnificent achievement visually. But the real key to the story's emotional impact is the comment it makes about prejudice and marginalization.
Humans tend to think in binaries like good or bad, rather than recognizing the nuances that make us all unique. The relationship between Glinda and Elfie is complex because the two characters are complex... just like most relationships.
The perfect "good witch" is not so perfect after all. She's self-absorbed and vain and presumes entitlement. Everything she thinks she's doing to help others is really for her own self-aggrandizement. So different from the "good witch" we remember from the original Oz.
Meanwhile, Elphiba is defensive and stubborn and off-putting, most likely suffering from PTSD. That the two find love for each other is a beautiful thing. That they find themselves in the future having to live up to more expected stereotypical roles thus losing that friendship is sad, indeed. As happens so often in today's deeply divided and binary oriented society.