In "Night of the Fright Hound", despite the robot dog being fast enough to keep up with the Mystery Machine, it took long enough for the Gang to hide within the machine factory while chasing them in hot pursuit. Since Jason's mom was controlling the dog, she obviously needed time to catch up to where they were at.
Velma thinks Jason had Scooby framed because the Fright Hound's parts look like something he would make. Jason's mom worked in military robotics, so it's very likely she taught her son what she knows about engineering, hence the uncanny resemblance between their works.
There's also how in Episode 11, it was Velma who said: "I guess we're not a team anymore". Who was the one who caused the gang to drift apart in episodes 25 and 26?
It was baffling that the gang STILL can't figure out that the "monsters" are people in costumes (usually). After watching episode 11, realization came that they have these beliefs because the adults of the town also share the same ideas, given that Crystal Cove is titled "the most haunted place on earth." There's also the fact the monsters in this series are the most realistic to date. The guys making suits in this one are frighteningly good at it.
The criminal's identity in "The Mystery Solvers Club State Finals" being The Funky Phantom makes so much sense in hindsight. After all, usually the criminal is someone pretending to be a ghost.
It sure was lucky that Aphodite's love potion didnt have an effect on animals thereby allowing Scooby and Pericles to gather the ingredients for a cure. Given the reveal that Pericles was the one who sent Aphodite the information on how to make the potion, this makes sense. He wouldn't want the potion to affect HIM after all.
When the Freak saves Fred's life, he just pauses and stands there for a second before turning to run, almost as if he didn't quite know what he was doing. It's possible he didn't. Mayor Jones' subconscious "better side" in the Sitting Room acted up when he heard his son's cries for help.
Why is this incarnation's Fred so obsessed with traps? For the same reason that he exhaustively keeps track of Daphne's schedule. From an earlier age, he's been told by his "father" that his mother abandoned Fred when they were younger, leading Fred to obsess over something that will keep his loved ones close and keep them from leaving him i.e. traps. Also functions as a Fridge Tear Jerker.
The plot point that there were many previous incarnations of Mystery Inc., many of which contain two men, two women and a talking animal mascot, is most likely a meta reference to the number of similar Scooby Doo-type shows Hanna-Barbera pumped out in the wake of Scooby Doo's success, not to mention the many incarnations of the show itself.
Blue Falcon acts like the dark and gritty The Dark Knight Returns Batman, who had been retired for years before going back into action. On a meta level, Blue Falcon had also been neglected for years before showing back up on this series.
Grim Judgement: There's a crack in Hebidiah Grim's facade of G-rated Slut-Shaming. While he attacks girls because of their necklines, make-up, and Leg exposure, he doesn't attack Velma and declares her to be un-tempting. If he was a crazed Puritan Judge attacking people for those reasons, he would have gone after her for exposing her legs. The reason he didn't was because Gary and Ethan don't find her attractive.
Why was Fred able to tell he was in a fake future right away from two simple clues when he's usually not good at clues? Simple! He was caught in a trap! And if there's one thing Fred would recognize right away, it's a trap!
The reveal that the current gang is the purest since the original makes sense when you think about some of the animal companions we've seen: a skunk, a bull, Professor Pericles the Parrot, an orangutan, a donkey and Scooby. Bulls and donkeys are known in media for being stubborn and singleminded. Orangutans and parrots are known for being smart and skunks are known being hot-tempered. All of these species traits were taken by the entity, made all the animal was about and then twisted beyond recognition. Then the twisting was used as fuel to corrupt the other members of the group. Scooby on the other hand is a dog and what are dogs known for? Loyalty, the first trait in an animal companion that the entity couldn't twist, and because of the untwistable nature of the animal companion, purity of heart was passed along to the rest of the current team. Meanwhile the first animal, a jaguar, is an animal sacred to at least one god of the time it existed in, so that likely meant it had been chosen by a benevolent Annunaki.
Ricky Owens probably became obese after growing up due to the fact that he eats so much, being the Shaggy of the original Mystery Inc. The new timeline in "Come Undone" has him in better physical condition, because he married Cassidy in that universe, so she probably reigned him in. Ricky's obesity is also a good look at what Shaggy would look like if his appetite catches up with his physique.
In the last episode, who are the ones that run the longest before getting caught? Shaggy and Scooby, the two that run the most.
In the new timeline that emerges in the final episode, the gang go off to it is heavily implied, relive the lives and adventures of Scooby-Doo, Where Are You!. One of that series' great mysteries was how in blazes the kids rode around with no concerns about money for food and gas. This new timeline, with even wealthier parents and multiple contest winnings for all of them, finally puts that to rest.
The series finale finally gives a justification for why the Gang was Walking the Earth. They were on their way to meet up with Mr. E and were simply solving the mysteries they've come across.
Did anyone else notice the physical similarities between the Nibiru Entity-possessed Professor Pericles and Char Gar Gothakon? Considering Harlan Ellison apparently developed supernatural powers from years of writing fiction, perhaps the idea that H.P. Hatecraft could see creatures from other dimensions isn't as far-fetched as it seems. Extra fridge bonus when you remember that the Nibiru Entity's real name was never revealed. Now what was the name of Hatecraft's book, again? Char Gar Gothakon: The Beast with No Name.
Even better? Ellison decides to team up with Hatecraft to write even more books. Perhaps he wants to see whether or not Hatecraft will also gain similar powers!
How did Mr. E sneak a message into Shaggy's sealed bag of chips without him knowing? At the time, it seems like some serious ninja magic, but given what we learn later on it makes perfect sense: he owns the company that manufactures them.
This does raise the question: How did he get the message into the specific bag of chips that Shaggy bought? Were there similar messages in every bag of chips?
Jason's father was never seen, so how's he going to support himself at home now that his mother has been arrested?
Not being seen doesn't mean not existing.
In the pilot episode, we see a museum showing the costumes of some of Mystery Inc's Rogues Gallery, including Charlie the Funland Robot. Unlike the other villains, Charlie wasn't a man in a costume, he was an actual android. At the end of his debut episode, he gets reprogrammed to act more friendly. This implies that even after his redemption, his creator, the caretaker, eventually shut him down for good and sold him to a museum. Of course, Charlie later comes out of retirement...
When Alice May was dressed as the prom ghost, she got awfully touchy-feely with her date before she kidnapped him. Now, since nobody was around to see it, that's not even part of the prom ghost charade—it's just Alice May herself. Considering the later revelation that she kept him captive and tied up for days...what do you think she was doing to him in that time?
If the vampire hadn't unmasked herself at the end of episode 11, Daphne would've unintentionally committed murder.
In "Grim Judgment" one of Hebediah Grim's targets is Mayor Nettles, an adult. Hebediah Grim is two teenage boys.
Episode 26 has Shaggy's mom telling her son that they're taking Scooby to a farm while He goes to military school, and it's revealed that this "farm" was the pound. That means that in this universe it is legal to completely uproot a creature with human intelligence (who can even talk), possibly never seeing their loved ones again, simply because you don't want them anymore. One wonders how they would treat the mentally ill...
In the haunted mansion episode, the youngest and only surviving member of the Darrow family lived alone for years, claiming his family died over time. What happened to the bodies? Did they really die over time? or was it that they all died at the same time and his memories blocked it out?
During "The Evil Heart" they take out all of the goons with Blue Falcon (long story). Then a few minutes after all of the exciting stuff the island is blown up. The gang escape on Dynomutt and the villains escape on jetpacks and you see the island explode. The mooks were knocked out when this happened. They are implied to be dead.
The Horrible Herd was released into the sea. The implications are referenced in show... But then you remember that Tom and Tubb, two children, often visit the ocean with their pet seal Scooby and their ship Moby. And the Horrible Herd are established to be nearly unbeatable. Thank goodness that ultimately any damage to the 'verse is undone by the finale.
In the final episode, It's not made clear what happened to the not-Mystery Inc. kids who the gang seem to have replaced in the new timeline.
In the new timeline, Daphne's sister's lives have been ruined... or at least severely downgraded from the success they made before.
On the other hand, it's heavily implied in 'Shrieking Madness' that they were pushed into university early, as four siblings graduating university at thirteen does sound somewhat improbable on its own, and we're never given any particular indication of how old they are. It may just be that, this time around, they're getting to live their lives and careers at their own pace and the Blake parents just hold their children to absurdly high standards.
We get some implications that Daphne's mother is genuinely insane, thanks to throwaway lines most viewers might not think twice about, usually jokes most kids wouldn't get and would go by too fast for adults to think too much about. Example paraphrased from episode 23:
The whole "police won't catch monsters because it's good for tourism." In the original cartoon, the whole purpose of the criminals dressing up as monsters was to scare people away so they could engage in their activities without intervention. And since Crystal Cove thrives on haunted tourism, it really doesn't make sense to use a tactic that is bound to bring mass attention onto themselves. When one further considers that the monster's activities were things that should scare away tourists (IE-people at a Renaissance Fair being assaulted and paralyzed by the gnome, two rampaging behemoths wrecking a popular night club), it only makes the show's constant hand waving through the Adults Are Useless theme even more frustrating of an Ass Pull.
Fridge Brilliance: Both the mayor and the sheriff are totally on board with monsters roaming around Crystal Cove committing crimes. Monster costumes in this universe aren't a way of chasing ordinary people away, they're a way of making police refuse to investigate your crimes. Most of the outfits are also directly useful in committing the crimes themselves (without the Gnome as a supernatural explanation for the paralysis, doctors might have been able to cure it; posing as the goddess Aphrodite gave victims a belief structure to hang their drug-haze on; and so forth).
Notable because it was intentional. When Alice May was caught, she revealed that she was the daughter of the Creeper from the original series, and is trying to avenge him. In her flashback, it shows her as a young girl when the gang caught her father, when she is the same age as they are. It is revealed that the whole story is fabricated as she is employed by Mr. E. They expected the gang to realize the Fridge Logic in a few days. Ironically, they don't, and still refer to her as the Creeper's daughter when they see her again. It must have taken all Alice May had not to laugh at them there and then.
Well, fair's fair, the gang can't actually see the flashback scenes in the explanations. They might have just assumed the Creeper had a daughter their age whom they just didn't know about.
Well the series ends with the entire gang being enroled into Miskatonic University, and yes, Scooby was specifically mentioned. Apparently talking animals can go to school with people.
Yantz specifically says, "I don't know why I let you take this class." So, presumably, Mystery Inc asked him if Scooby could attend.
Episode 26 has Mayor Jones stare sadly at a picture of his wife/Fred's mom. We later find out that she's from a magazine and Mayor Jones was never married. Fred was stolen from Brad and Judy from the original Myster Inc. So why is he staring so lovingly Perverse Sexual Lust?
It could be just 'What am I doing?' because he's using that picture as a lie to hide what he's done. It's up to interpretation but that could've been foreshadowing that he really did 'care' about his 'son's safety.
If he IS listening to an inner conscience, then it gets shut up pretty quickly. He dons The Freak costume minutes later to protect his secrets.
In episode 26, we learn that the first piece of the Planispheric Disk is recovered by the original Mystery Inc. some 20 years prior in the caverns beneath Crystal Cove. However, Pericles is later said to have acquired the coordinates that lead them underground using information gleaned from the Planispheric Disk pieces in the possession of the current Mystery Inc. and Mayor Jones. In other words, he got the coordinates off of the two pieces that they didn't yet have!
Until you realize that he's a Magnificent Bastard and probably wrote that well after the fact as a lure to bring the original back under his control.
So... Fred kept all of his fake father's stuff after Fred Sr. was arrested? Given that he probably had Fred designated as his legal heir, that kinda makes sense. But why did Fred move out instead of kicking his parents out? All of his friends still live in the same places before, so it isn't like he's trying to hide.
Pericles has broken into the house before. So did his parents. It's also possible that Brad and Judy have installed new traps/modified some of Fred's old traps he's put around the house. It's a big isolated space that their enemies know intimately. It's just not a good idea to stay there.
... Why did they kick Hot Dog Water out of the group solely because Daphne rejoined? Does it have to be only 4 humans and a dog?
According to Nova/The Annuunaki, yes, there HAVE to be four Humans and an animal.
Also, the evil entity is the one that makes it that way. It was manipulating the gang's actions in kicking Marcie out.
How on Earth did the conquistadors make or find that multiple layer inter-dimensional hiding place / prison under Crystal Cove for their treasure?
The good Anunnaki could have helped them. One way it could have happened is described in the fanfiction story Disk Mania.
Since in the new "universe" without the Entity all the crooks from Crystal Cove never used monster masks, what happened with Gatorville? Were they influenced too by the Entity or if not did they still disguise themselves as Gators?
They were probably close enough to be influenced. And there might not have even been a Gatorville, if the gators were a supernatural side-effect of the Entity's presence.
Since all the Scooby-Doo Hoax cases were created by the Evil Entity, how can they expect to find any mysteries of the sort they enjoy on the road at all? Logically speaking, they should find nothing but ordinary crimes (and few of those if no Weirdness Magnet is in operation for them, and people don't have any reason to ask for their help based on their reputation). This should not be the start of Scooby-Doo, Where Are You!, but of a long period of boring disappointment for the gang. Perhaps Nova or other good Anunnaki will intervene to give them cases.
Mystery Incorporated shares a setting with Johnny Quest and the Blue Falcon and Dynomutt. There's still weirdness and out and about. Besides, while the Evil Entity is gone, that doesn't mean that other threats won't come forward. The new Mr. E, at least, seemed to think he had some work for the gang.
There may be some remnants of the original universe. Mystery Inc. (and Harlan Ellison) remember it, after all. The monsters the gang discovered before the series began (the Creeper, Charlie the Robot, the Space Kook, etc.) still do turn up in the new universe, just scattered throughout the country and the world. The world itself is still recognizable despite the retroactive change of hundreds of years of history. The concept of dressing up like a monster to hide your crimes may be a part of the human consciousness, even if the costumes are far less convincing now.
In the alternate reality why is Fred's name still Fred. Sense he was raised by his real parents and not Fred Jones Sr. , wouldn't they have named him something else?
Someone (Nova?) seems to have intervened in the reconstruction of the timeline to make things better for all concerned, and for the gang in particular. It doesn't seem to be just the world that would have resulted with no Evil Entity (with changes going back to conquistador times, there was no guarantee that the gang and their friends would even be born). The stability of Fred's name is just one minor intervention. What is more interesting: did the pre-Nibiru Brad and Judy actually name him Fred, or did they just decide to keep calling him that for convenience?
Keeping in mind that other universes have existed, with Fred's last name being Jones in them, it's hard to imagine that his first name would change.
Getting into WMG territory, but perhaps Brad and Judy are close enough friends with Fred Jones in this timeline to name their first son after him.
Fred continued to use the last name Jones, even after he found out the truth about being kidnapped as a child by Fred Jones Sr. Now, in the new timeline, he'll probably keep getting in trouble for using a fake name. He is and has always been Fred Chiles according to this reality, and all his legal documentations will reflect this. But he's still going to think of himself as Fred Jones
In the past of the Nibiru reality, the gang encountered a variety of different monsters that were then put on display in Mrs. Dinkley's museum — the Creeper, the Space Kook, Charlie the Robot, etc. If the new reality is Scooby-Doo, Where Are You!, then they're going to run into all those monsters again ... and not recognize a single one of them. "Foul Play in Funland" would have been a lot shorter if the gang's reaction was just "Oh, Charlie the Robot's acting up again" ...
Well, since we didn't see how most of those classics played out in this world, we don't know how big the differences were.