I'm seeing lots of Halo posts being disappointed with certain decisions in the series, and all I can think of is how the Halo TV show had the birth of Cortana from a doctor blending (as in, a blender) a clone of themselves to create a chip they inserted into Master Chief.
I consider Cortana's unashamed nudity to be an integral part of her character that speaks to both her competence and divinity in the mythos. It contrasts heavily with the other protagonist who is sealed head to toe in MJOLNIR.
Halo 4 understood this dynamic well.