They're still keeping the action largely indoors, on standing sets. The Phantoms are spreading, but we don't see them until they converge on the tower. We didn't even see them capture Silas's Phantomized roommates.
Lena quitting LuthorCorp is a decision that makes sense in terms of the personal reasons she gave, but it's dangerous to leave Lex free to do what he wants with the company. She may be right that his hubris will be his downfall, but he could drag a lot of other people down along the way. Anyway, I'd read that Lena was going to become a full member of the "Superfriends" this season, and I guess this is how they set that up.
When Alex was despairing and then we learned that the Phantoms induce misery in their hosts, I thought it was going to turn out that Alex was possessed too. I'm glad they didn't go that route, that they let her depression be a genuine emotion she had to work through.
You know what just occurred to me. In the last episode, Brainy said that all the phantom zones from all the multiverse converged into one after Crisis. That means everyone who was sent there in all the DC mediums are in one place. What big villain do we know is there? Faora from Man of Steel. Make it happen Supergirl.
Rather, he said the opposite of that -- while the main universes (at least a few of them) converged into one, the Phantom Zone split from one into many. So now it's a multiverse (or a multi-pocket-universe) when it wasn't before. It's fragmented into mini-Zones, and that's why they can't find Kara.
Is Argo no longer a thing? Kara mentions she and her mysterious cousin are all that is left.
She said, in telling her backstory, that she grew up believing she and Clark were the only ones left. She was speaking of the past, not the present. She brought it up to give context for what it meant to her to find her father alive.