Well, I expected that "The Bottle Episode" would involve Kandor in some way, and I was close -- the same idea of Brainiac bottling cities, but revised to his whole species bottling whole planets. And the bottled planet ends up stored in the Fortress of Solitude for safekeeping, a nod to Kandor.
It's bothersome that the characters were talking about the whole multiverse ceasing to exist, when we know from the closing montage of Crisis that it is still out there. It's just a few Earths that merged, and all the other distinct worlds are still there. (Obviously the ongoing ones like Lucifer, Titans, Doom Patrol, and the DCEU still exist, and the producers confirmed that Smallville's world still exists, so presumably the rest do as well.) And it's odd that they don't have the means to determine that, since we saw them freely scanning the multiverse in Crisis, and back in Arrow a few months ago we saw that even some random disreputable Earth-1 scientist had the tech to determine that Earth-2 was destroyed. So it's a strange storytelling choice to have the characters believing something that we know is untrue, and not to give any indication within the episode that they're wrong. It confuses the issue.
But they made an interesting choice with Brainy to reset him to something more faithful to his comics incarnation, and to explain why he'd been different from it before. It's certainly an improvement to his makeup design, and a simplification, so I hope that means we see him in his true form more often now. His constant use of an image inducer to look human is something that's never made a lot of story or character sense, and I figured it was something they only did to spare Jesse Rath from having to spend so much time in the makeup chair. But now that it's just green paint and a wig, it should be a much quicker makeup to apply, so there's less reason not to use it, and with his greater self-acceptance, there's even less character reason for him to hide his true form.
I'm also a little disappointed they got rid of Female Brainy so quickly. She was the most impressive one of the bunch, and kinda hot. And it was a nice touch to cast Rath's sister as his gender-swapped doppelganger. They've played brother and sister before, but never the same character.
Although the revelation that Brainy's really green and that the "dots" on his forehead aren't a natural part of him raises questions about Brainiac-8/Indigo from season 1. She also had 3 forehead lights and was deep blue (or rather, indigo), but surely those weren't the same kind of behavioral inhibitors, since she was hardcore evil. There's also the unresolved question of how Brainiac-8 existed in the past/present if Brainiac-5 is from 1000 years in the future.
But then, a lot of plot threads from season 1 have been ignored ever since -- Maxwell Lord, General Lane, the Omegahedron, etc. And now that the timeline's been rewritten, they're even less likely to be revisited.