It's hard to tell what a new season is going to look like based off of the season premiere. Most of the time they use the first episode to clean up any cliffhangers and set the show back to status quo. This was always prevalent on X-Files where the season finales showed us hard evidence and Dana Scully was amazed only to have the genie put back in the bottle with the next season premiere and Scully return to being skeptical. But with the second episodes now in, we can look at what may be in store this season of the Arrowverse.
It's interesting that a show that has a good number of aliens in it has decided that the theme for season three should be humanity. Unlike the other three shows, there really was no cliffhanger to deal with going into Supergirl season three. The Daxamites were defeated and Mon-El was shot off into space. We don't know what happened to him, but we don't need to right now. The show had to deal with the ramifications of the finale though both on the city and on Kara Danvers.
The focus of the first episode was Kara trying to distance herself from her humanity. Which is an interesting word choice. This isn't a situation like with Mr. Spock who was half-vulcan and half-human. Kara Zor-El is Kryptonian and was raised that way until her early teens. While Kal-El has been immersed in Earth/human culture his whole life, Kara knows Kryptonian ways from the years she was on the planet. And also unlike Spock, Kryptonians aren't based on logic and force down their emotions.
What they're talking about is the human behaviors that she has picked up since she's been on the planet. Similar to those behaviors picked up by J'onn J'onzz and Reign, which will play a huge role this season. They're spending time building up Reign's life as Samantha Arias. She is a single mother trying to balance taking care of her daughter and running L Corp for Lena Luthor. As her powers surface, it is likely her base instincts will return as well, making her the Worldkiller she was engineered to be. But her learned humanity will likely be the key to stopping her.
I think we're going to see a similar storyline with J'onn as he deals with his father M'yrnn who will undoubtedly question the changes in his son. As much as the main story will be the two Kryptonians battling it out as both Supergirl and Reign and also as Kara and Samantha… the father/son relationship will parallel the old ways / new ways storyline as well.
The key to this season may not be any of the above characters, but how the human characters around them react and interact with them as the season progresses. Supergirl's support team of Alex Danvers, James Olsen, Wynn Schott and Lena Luthor will likely be the difference for Kara and in some ways for J'onn.