There seem to be very few people out on the streets of Gotham. While this can be attributed to the limitations of CGI shows, the setting is Gotham, a city well-known for how corrupt and shifty it is, so there would likely be few people on the streets.
Some places that are less busy than others, especially at night. Criminals would stick to the quieter areas — and since crime is the show's focus, that's what we see.
In "Secrets", Magpie's goal was to regain her lost memories, or her identity. She also has an obsession with shiny objects. A person can see their reflection in shiny objects, so Magpie was both literally and figuratively trying to "see" herself.
Also, the lost identity was that of a kleptomaniac. Magpie's obsession might be the same subconscious urges that Margaret Sorrow tried to suppress re-expressing themselves.
Humpty Dumpty's rhyme is a metaphor for his life. Humpty sat on a great wall (being right in the middle of a turning point of the war between Whale and Gordon), then he had a great fall (his descent into madness), and all the king's (Gordon's) horses and all the king's men (cops and doctors) couldn't put Humphrey Dumpler back again (he is irreparably insane).
Bringing in minor villains to make them more recognized? Seems like a totally new concept for Batman, right? WRONG! Batman: The Animated Series did this once, too. It took a villain who nobody remembered out of the mothballs and retooled him into a much more interesting character. That villain's name? Mister Freeze!
In addition, the previous Batman series Batman: The Brave and the Bold did the same thing, though on a much larger scale by also incorporating obscure DC Comics characters in general.
It's mentionned that Humphrey Dumpler's grandmother died in mysterious conditions. Take in account what happened to her in the comic...
"Reckoning" has two:
The ending of "Reckoning" strongly implies that the souls taken by the Soultaker Sword can be liberated, but can never return to their respective bodies. This pretty much means that recurring characters Jason Burr, Bethanie Ravencroft, and Silver Monkey have been Killed Off for Real.
"Reckoning" also has a four-way fight between Professor Pyg and Mr. Toad, Magpie, Cypher, and Phosphorous Rex that plays out off-screen. Pyg and Toad are the only two of those characters that are ever seen or mentioned again after that episode. Think about it.
Also a bit of Fridge Brilliance — the two villains who work as a team were the ones still standing when the dust settled.
In the final scene of the show, Anarky is seen playing a game of chess with the notable heroes, villains, and important characters of the show as game pieces. If you look very carefully, one of the pieces is shown to be Barbara Gordon. Either Anarky knows about her alliance to Batman and Katana as Oracle, or he's possibly targeting her due to being Gordon's daughter.