It doesn't require much thinking to realize Johannes van der Berg is Hastur given his bright yellow clothing and Obvious Judas nature. However, it proceeds to become even more surprising when you realize just how much he's manipulated events up until this point.
"A Frosty Welcome" doesn't give an easy answer to whether Lewis Flynn was guilty or not but the nature of the crime indicates the truth. If he'd killed Albert Throgmorton in a rage, he wouldn't have shot him in the head, hung the body from a noose, then hidden the body in a warehouse.
The motor boat the player character is using is called Cyclops II This isn't a random reference either, as Reed served on the USS Cyclops and was the Sole Survivor of its sinking.
It's very likely that Johannes procured the boat and gave it this name simply to mess with Reed.
A kind of amusing in-universe one is that Chief Lyons hates Charles Reed for breaking into houses, firing his weapon countless times, stealing objects from any open drawer he finds. You know, the way any police officer would treat the behavior of a player character.
Robert's disgust and loathing toward the Innsmouthers may seem like Dramatic Irony or Hypocrisy given his Half-Human Hybrid status as well. However, Robert's family is clearly aware of the occult and familiar with the Blackwoods. Thus, more than anyone, he knows that the Innsmouthers are worshipers of Cthulhu and thus part of a Religion of Evil determined to bring about The End of the World as We Know It.
Robert Throgmorton's Cultural Posturing actually may be necessary to protect his social position. Lording over the rest of the city with his wealth, status, and power could be the only way to avoid being ostracized. It's the 1920s and most of America would not tolerate a man with a "foreigner" mother. Human or otherwise. Robert rubbing his heritage in everyone's faces with statues of gorillas, tribal art, and more may be a way to intimidate Oakmont's residents into backing down.
If you do a favor for Anna, you are sent down to the basement to meet with the leader of the EOD where they try to kill you. It never occurs to Reed that Anna is the leader of the EOD after the Blackwoods have disappeared and she sees right through him.
Graham Carpenter is easily taken in by the Redemptionist Church because they go to pretty elaborate lengths to disguise the fact they're a Religion of Evil. They cast illusions on all the statues of Shub-Niggurath to appear as the Virgin Mary, hide all of the bodies, and engage in a lot of "love bombing."
Reed's suicide not working to stop the Cycle makes sense in that there's The Chosen Many. They only need one but losing Reed just means they have to find or create another.
Cythlla being underneath Oakmont helps explain why everyone is so blase about the supernatural.
Reed is frequently described as carrying the Dreamer's Seed, and several documents confirm that the inhabitant of Cthygonaar is Cthylla, Cthulhu's daughter. Cthulhu the Dreamer. Who will be freed by being reincarnated from his daughter's own womb. So, in essence, Reed has been infected with Cthulhu's sperm, which is compelling him to go to Cthulhu's daughter and impregnate her, with himself. Ick.
You can find the Yellow Sign in Granny Weaver's basement. Is she guarding Oakmont's secrets under Johannes' instructions?
Also a moment of awesome by the developers, the undersea grotto you dive into during "Lost at Sea" has a lot of stone formations that you pay no attention to. However, if you stand just right at a photography point, you will realize you're staring at a statue of Great Cthulhu himself.
George believes the police would never side with him against the EOD. However, if you've worked with Robert Throgmorton, then it's very likely you know the police hate the Innsmouthers and would get his full support in going against them. Thus his plan is entirely pointless.
"Quid Pro Quo" has George Cavendish present his plan to poison potentially hundreds of Oakmonters in order to turn the public against the EOD. This will cause a famine as the fish brought in by the Deep Ones is the only thing keeping the public alive right now. That's in addition to the deaths by poisoning. He also plans to turn himself in for the murders which, when exposed, would undo all the damage from framing the EOD in the first place!
George did succeed in causing the EOD to shut down their charitable operations as the poisoning of the fish ended their efforts. It just causes a famine in Oakmont.
This isn't a random reference either, as Reed served on the USS Cyclops and was the Sole Survivor of its sinking.