good story so far. give more chapters, please.

The S.E.L.'s voice sounds female in the game and claims the eggs as her own, also the eggs being there in the first place suggests that they were laid in the facility, ergo the S.E.L. is female.

As for the S.E.L. only knowing some human concepts and not others she only got bits and pieces of info from Jack, so there are gaps.

Name suggestions Emma, Emmie, Levi, Marina, and Abby.

Why would anyone complain about The Sea Emperor being female? Its canon, also mabye a name of an emperess of a great civilization could be nice for her

Woah!~ I was not expecting a crossover concept like this, but the way you wrote this up makes the two fit so well!
(Ps, LOVE Jacks YouTube series, and a humerus way to start a new story based of the SubNautica universe!~ :D )