Batman must have lined his utility belt with lead, which would explain why he was able to keep Kryptonite in it without Superman noticing. It makes sense since Batman was also one of the first people to figure out that Kryptonite emits a small amount of radiation that is also fatal to humans after prolonged exposure, so he probably did it (initially) to protect himself. This is further backed up in the episode, "Knight Time" when Superman had to masquerade as Batman, and Robin had to tell him which compartment in Batman's utility belt that the grappling gun was located. Superman, having x-ray vision, should have spotted it unless something as dense as lead was blocking it.
A small one in "Livewire". When Leslie is hosting her concert during a lightning storm, notice how in that split moment, a lightning bolt was headed towards her note It almost hit her, before Superman took the brunt of the strike . Now a little science lesson on the side: lightning can be positively or negatively charged. It may be coincidence, but if one imagines the lightning bolt was positively charged and was attracted to a negative charge on the ground, chances are it was attracted to a negatively toxic influence like Leslie.
Other incarnations of Superman (e.g. Superman Returns) have pointed out that, despite having inherited advanced Kryptonian technology from his biological father, Kal-El doesn't share any of it with the rest of the planet when it would have helped people. Well, the DCAU offers an explanation spread across its continuity; very few things originating from Krypton are safe for humans to handle at all, and those few things eventually become harmful to humans unless additional safety precautions are put in place. Superman is shown collaborating with scientists to study Kryptonian biology and tech, but it will take time to adapt any of it for safe human consumption in a way that villains like Lex Luthor can't transform into a weapon of mass destruction.
In this continuity, Supergirl isn't from Krypton but from another planet in Krypton's solar system called Argo (a nod to the city of Krypton that the main continuity Supergirl comes from). At first you have to wonder how could the Argonians develop powers and abilities similar to Kryptonians under a yellow sun and even have vulnerabilities to Kryptonite if they're not from Krypton. However, Supergirl's mother, Kara Inze, called Argo Krypton's sister planet and this was very likely not metaphorical. It's very likely that the Argonian's were descended from Kryptonian colonists that terraformed Argo some centuries ago. It's also very unlikely that it's been long enough for the Argonians to become so genetically dissimilar to Kryptonians that they can be considered a completely different race. Further, the environment, Flora, and Fauna are probably an exact match for Krypton based on terraforming which mean's that, environmentally, Argo is another Krypton. Lastly, since Kryptonians have FTL capabilities, migration between the worlds is probably as simple as an airline flight for humans on earth so Kryptonians and their counterparts on Argo probably travel between their respective worlds and intermingle quite regularly. Thus, even though Supergirl is an Argonian and not from Krypton, genetically, she is for all intents and purposes just as Kryptonian as anyone born on Krypton.
On the surface, Clark's "Excuse me?" reaction to Lois' "nice 'S'" comment appears to be him being taken aback at having his picture ogled. However, it might also be genuine confusion about the innocent literal statement — his logo is (as in most modern continuities) a Kryptonian symbol that just happens to resemble the letter "S", and the connection simply might not have occurred to him (especially considering that this happens before anybody calls him "Superman").
When you think of Jor-El's plan to save Krypton, it's downward chilling: Put everyone in the Phantom Zone, then once Jor-El travelled to Earth, he would release his people. Two words: Alien Invasion.
Also remember that The Phantom Zone is where the most vile and evil Kryptonians are imprisoned. This could have been a fate worse than death for many innocents. Its no wonder why the Kryptonian council rejected this.
Then again, Jor-El's plan might've included the idea of letting the criminals in the Phantom Zone out of there and onto the dying planet while the rest of Krypton stays in a safe stasis.
Unlikely, given Jor-El isn't the sort of person to murder criminals who are serving their prison sentences. But that brings up another bit of horror: think of all the criminals in the Phantom Zone who didn't have life sentences. Let's hope Clark checks up on Krypton's legal records, otherwise they'll be trapped in the Phantom Zone forever - and if they do come out, they'll learn that their friends, loved ones, and entire civilisation are all gone.
This is also unlikely as the Phantom Zone is reserved for dangerous crimials who have done serious crimes. This means that the Phantom Zone is more like a maximum security prison so the only criminals in there are the dangerous ones with a long sentence. Supes should still check on them but be careful as most if not all of them weren't the nicest people to begin with.
Regarding "The Late Mr. Kent", some people might wonder why Clark didn't just create a new Secret Identity if it was so important to him. After all, he mentioned doing the same thing when Mxyzptlk threatened him with revealing it in an earlier episode. However, not only would that put Clark in the position of presumably having to contact someone criminal to create a fake identity trail for him, but it would also mean completely cutting himself off from every connection to his old identity. He wouldn't be able to clear Ernest Walker (at least, not without outing himself); he'd have to find a new job, quite possibly in a new city, without access to Clark Kent's bank account. He wouldn't be able to tell his friends and Lois that he's still alive; he wouldn't even be able to visit his Ma and Pa without putting them at risk!
We don't know how long the brainwashed Superman has been under Darkseid's servitude. Just how many atrocities Darkseid manipulated Superman into doing? Just how many aliens Supes had terrorized and conquered?
