I don't think Tusk and Momoka are dead and it is fine.
Cross Ange deals heavilly with alternate realities, time paradoxies, and the duality of life and existence.
I think the anime is doing what it does best, and that it uses the main character Ange, who is the only person constant throughout all these time paradoxes, as a way to mold her. She, just like Embryo, has seen multiple endings to life, multiple histories, and experienced love, lust, betrayl, and comraderie during her time alive.
These deaths were needed, and unlike in AZ, when the characters come back to life, I won't find it cheap. Because Cross Ange the series uses this stuff for development of a character in the truest sense.
Steins Gate did this. Although they all came back to life in the end, what Okabe witnessed forever changed his demeanor, and perception on life. Whereas he had a near disfunctional view of society and life before the incidents, he came out of it...a real 'man'
Cross Ange does this quite well. Where Ange too also came from a place with a disfunctional view before meeting all the adversity that would in the end, produce one of the strongest female leads in the last few years.
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