I think it's basically that "outsider" thing that I relate to so well (I think most of us do :P). Elphaba is green (can you think of another G word?) and it makes her stand alone from her peers. She's been bullied and ostracized all her life for it, but still manages to have a certain strength about herself. She doesn't give too much of a fuck what people think about her, otherwise it would get her down too much. She's someone who society doesn't think is strong enough, but in the end, she is the one walking away, her battle won (in an indirect way). She doesn't bend over backwards to fit into society; she has no problem with being herself.
Another reason why I love Wicked is that it's the story of someone who doesn't consider themselves attractive, but someone loves them anyway. I recently learnt the same lesson. If someone is capable of loving you, even if it's for a short while, it might mean that you aren't as unattractive as you first thought. Even though Elphaba puts up a front of being so strong, she really does consider herself "beautifully tragic" (compared to her sister's "tragic beauty"). So when Fiyero tells her she's beautiful, she doesn't believe him. However, eventually Elphaba learns to accept and love all of herself.