[Jan-Poo]

Originally Posted by serenade_beta

Some guy who probably appeared at the end of the last episode but I completely don't remember because this show: "I have a daughter, but she's like a son!"
Protagonist: "That makes sense"

Me: ................? These lines don't work when you skip character development!

Small spoiler about Muv Luv Extra (which is the first story of the Muv Luv universe that this show skipped and somehow assume you already know), to explain Mikoto's whole deal.

Spoiler for Muv Luv Extra:

During the whole Muv Luv Extra story Yoroi Mikoto is presented as a boy and "he" takes the role of the classic MC's best male friend that is present in almost every school life eroge. There is therefore no route for that character, because you cannot romance "him" at all. That being said Mikoto always looks somewhat feminine even in that situation, and the name also appears very feminine before you are told the actual kanji used.

Then when Takeru is transported to the other world, both in Unlimited and Alternative, Yoroi Mikoto is officially a girl as you can clearly see in this show.

As far as I remember Takeru never considers the possibility that Mikoto might be actually a girl in his original world as well, but the father in Alternative talking about Mikoto as a son, suggests he's the kind of crazy parent that would raise his daughter as a male.