Hmm.  First off, let me confess that I haven't read Seinen Kakumei Utena yet -- I almost never read fic, even very good fic -- so I'm only responding here to the idea of Utena having a sex change, not to your story where it happens.  There are a lot of plot ideas that I really don't see that can be made to make perfect sense in a well-written fic.  But as far as the idea, color me skeptical.

I would differ with you about at least a couple of the assumptions you make above.

- Does Utena buy the lie, fed to her by Akio and Dios and Anthy, that only boys can be princes?
You believe yes.  My gut says no.  Practically everyone in the series tells Utena that girls can't be princes, yet the only time we see her come close to acceding to that idea is in episode 11, when Touga convinces her that she'd rather be a princess.  But episode 11 is followed by episode 12.  So we have seen Utena be psychologically resilient: she responds to loss by retreating into femininity (not masculinity), but is soon called back to herself.  I think a similar outcome is very plausible after the final episode of the show.  Utena definitely has a complicated relationship with masculinity, but we never see her wish to be a boy -- and I don't see any text that supports your reading of her final line, which seems to me to be about not being strong enough or not being a good enough friend, not about not being a boy.  (As an aside, movie Utena cross-dresses -- well, yeah, so does series Utena.  That's nothing new.)

- More fundamentally: Will Utena still even want to be a prince when she wakes up?
You assume yes.  My gut says no.  In fact, my gut says that Utena hasn't been trying to be a prince for about two episodes by the end of the show.  Princes rescue innocent damsels.  They don't ordinarily rescue witches, particularly not witches who have stabbed them in the back.  In spite of her final lines, Utena's actions in the last episode are not consistent with those of a prince; they're consistent with those of a devoted friend, which the series explicitly contrasts with a prince by showing how Dios saves strangers while neglecting his sister.  Anthy is no longer a princess or damsel in distress to Utena, but a friend.   I don't think Utena will ever stop wanting to do good, but I think that once this moment of immediate and devastating loss passes, Utena will abandon the idea that she needs to be a prince to do good.  This is part of passing into adulthood.

Just my couple of cents.

Hi Satyreyes:

It's okay if you don't read fanfics; but perhaps my first post is not precisely worded enough, that you seem to misunderstand it in very significant ways.

- Does Utena buy the lie, fed to her by Akio and Dios and Anthy, that only boys can be princes?
You believe yes.

Umm . . . I don't exactly believe that, and I'll elaborate on why in the coming part.