Alex's evolution from mild internalized homophobia into out and proud is a linear progression any gay person hopes to have. The struggle that comes with upsetting the image your parents hold is a commonality that the show works through nicely. Although her relationship with Maggie ended, there's still hope for a happy and gay ending as Supergirl comes to an end.
Maggie's story of estrangement from her parents after coming out is a sad, but an honest reality for some people. Although, you never would've guessed by her courageous and strong unforgiving lesbian identity. Her badassness as an FBI agent transcends into her badassness as a role model for so many women who may struggle with environmental and internalized acceptance.
Nia is suffering at the hands of her nightmares which Brainy forces her to explore since he knows what she's up to in the 31st century. Eventually, they help her control the future.
Braniac-5: Well the good news is, her mind is active and alert. Alex: Oh, thank God. Braniac-5: The bad news is, she is very angry. Winn: Well, I'm sure she loves being trapped inside a mind prison.
You had me fooled, Danvers. I thought you were a soldier. But then I find this out. All the lies you must have told. You have undermined everything that we stand for, all to protect your own sister. Supergirl.