The Simon/Nia argument in the last episode of Gurren-Lagann is pretty much the Fakir/Ahiru argument in the last episode of Princess Tutu. Yes, they could not be 'together' in the natural sense. But they still had happiness, and it is by their choice.
Fakir chooses not to abuse his power by turning Ahiru back into a human, because Ahiru is a duck, that is her true form, and she's accepted it as who she is. Fakir would never turn her human, and that even if he asked her, Ahiru would say no. So to do otherwise would make him the same as Drosselmyer, playing with the fates of others. Simon knows Nia would refuse to him extending her own life, as doing so will only place him on the ground of the so feared Spiral Nemesis or even the Anti-Spirals themselves.