Revolutionary Utena is one of my all time favourite animes.
I'm glad someone else has at least seen it.
The last episode leaves a lot to interpretation. You can think she died or you can think she's still alive, but elsewhere. I can definitely see why she could be considered dead: the story of the boy that saved the little girl, but drowned himself. Utena is the little boy that commits this self-sacrifice. In whatever sense, she is dead to the acadamy and "forgotten".
Don't be afraid to see the truth, even if no one wants you to. Be yourself and not a fool. Don't ever be afraid to speak your mind and listen to criticism. Dissent is keeps our country progressive and willingness to challenge yourself is what keeps yourself ever evolving.