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.
Similarly, Fred believes that marriage is miserable yet something to aspire for. We later learn that Fred's mother supposedly left him and his father. Does Fred think that his mother left because his father was a jerk?
In "Grim Judgement", the soccer players' demonstration of historical ignorance at the end makes perfect sense, because it explains why they'd choose a pilgrim as their mutual ghost-identity, despite being on the West Coast where there never were any.
The reason that people do criminal activities in costumes in Crystal Cove is because that they won't get caught by the police because they support the tourism.
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. They also tend to be much more violently-destructive than in previous series, meaning that even if they are suspected of being fake, they're still plenty dangerous and merit running away from.
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, and he needed Scooby's help to haul the items he really wanted away, even if the dog didn't know what he was carrying in his pack.
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.
Or if he didn't spend so much time running away from the Monster Of The Week, which is bound to burn off a lot of calories.
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?
Maybe he broke into (or sent someone to break into) Shaggy's house and leave the bag for him.
Considering it turns out in Season 2 that dreams do hold some truth to them and can be transdimensional in nature, perhaps "Mystery Solvers Club State Finals" wasn't entirely built on nothing but Scooby's imagination.
Angel helps the remaining members find the kids. It turns out that she's Cassidy and she misses her friends. Her presence in the episode represents the original Mystery Incorporated.
Jabberjaw could be a descendant of a shark that got possessed by an Anunnaki. Likewise Boo the cat.
In "All Fear the Freak", Fred goes from still having faith in his dad at the jail scene to having strong mistrust of him two scenes later. The jail scene ended with Fred telling Shaggy to prepare his disk piece and Velma to prepare the map while Mayor Jones was in earshot. The next scene was of the Freak attacking Shaggy and Scooby at their house in an attempt to steal the piece. Offscreen, Fred probably realized that his father being gone from the house at the same time the Freak was at the Rogers' residence was not a coincidence.
The Nibiru Entity indirectly caused his own demise by manipulating the mystery groups to serve his purpose. Basically, he would have gotten away with it if it weren't for those meddling kids.
Mayor Jones emphasizes athletics to Fred, such as being doing soccer and wrestling. Given that it turns out Mayor Jones was the Freak, it explains how the Freak can move from one place to another and climb rather quickly without any obvious use of gadgets, — he has athletic background himself.
He doesn't have any gadgets (that we know of), because as he explains in his confession, his original intent behind wearing the Freak costume was to hide his identity while hunting for clues and scare off anyone that came across him while he did so. When he scared off the original Mystery Incorporated, all he did was corner them and talk to them. Besides, we already know that he doesn't have that much intuition in using other tools like the Internet anyway.
He doesn't use any gadgets against the new Mystery Incorporated either, because he presumably hadn't used the costume in years and it was an emergency.
Wanting Fred to do athletics comes back to bite him in the ass when Fred manages to catch up with him while climbing the cliff and running away. Not to mention the fact that Fred has been more physically active & traversed different environments than Mayor Jones has been as well as the possibility that Mayor Jones wasn't used to doing so much while in costume anymore (combined with that he was soaking wet and cold from being in the water a few moments ago, with Fred possibly being used to it).
Becomes significant in the series finale when it turns out he's a soccer coach for the high school team in the new universe.
In "Wrath of the Krampus", since it gets explained that Mayor Nettles went to the prison herself to recruit Mary Ann into the scheme, it makes sense that she probably talked to ex-Mayor Jones to recruit him, since Fred implies that the gang weren't the ones that talked to him. Of course, Fred can't bring himself to talk to 'his father' right now, Shaggy sucks at talking to people, the rest of Mystery Incorporated always thought he was obnoxious, and Sheriff Stone probably can't bring himself to talk to his criminal boss either. Mayor Nettles was probably the best person to talk to him, since they can't riff on each other besides being each others' replacements and she's smart enough to know how to persuade him (i.e. something like "Fred told me I could trust you, and now I'm not so sure.", implying that Fred still loves him, though an alternative interpretation that he won't consider is that Fred knows how greedy he is). Like him, she's a politician, after all. They speak the same language.
In the series finale, we learn that Brad and Judy became obstetricians rather than trap-makers. This isn't as random as it might seem: traps are what you use to catch something, after all, and a mildly self-mocking term used by some obstetricians to describe their duty is "baby catcher".
Thanks to the Nibiru Entity's malign influence, Scooby's predecessors within the various Mystery Gangs have a long history of betraying their human companions out of uncontrolled greed for the Disc pieces and/or treasure. Scooby-Doo seems to be entirely immune to this effect... except that he does have greed as one of his most salient traits, not just in this series but throughout the franchise. It's just that in his case, it's greed for food, not wealth. The freakin' Nibiru Entity aimed its mind-corrupting powers at his dog-brain's "want-stuff" neurons, but hit his "want-food" neurons by accident!
Did Ricky really come up with his codename of "Mr. E" himself, or was it perhaps modified from an Affectionate Nickname? It's common for close ones to call someone by an even shorter nickname using a syllable in their name, like how Marcie sometimes calls Velma, "V". Cassidy calling her boyfriend/husband, "E", wouldn't be out of character for her.
And Mr. E. does call her "my sweet angel" a couple of times, which points to Cassidy getting her disk jockey name from that.
You'd think that Scooby, Shaggy's best friend and loyal dog, would understand Shaggy taking up a romantic relationship with Velma. But Scooby is still a dog, and dogs in real life are known to get jealous and upset if their owners' attention is diverted to something else, like another dog.
In "All Fear the Freak", we learn that two years before Fred was born, Mayor Jones was a college student, and Word of God says that he later became a college instructor for a while. And given that in "A Haunting In Crystal Cove", it's never outright stated that Fred's fake mother was also Mayor Jones's ex-wife and it's also suggested that she ran off. So, from an outside standpoint (i.e. the general public), a rather adult implication is that Fred was conceived from pre-marital sex. And considering no one had seen Jones hanging around with a lady friend the past nine months prior to him having Fred (unless he already kept details of his personal life under wraps, since he's also shown to be a private individual), that also implies it was a one-night stand or a brief fling. It also looks rather interesting if he was still a college student or instructor when it happened.
If Fred figured that out, it would also contribute to his Daddy Issues, because this would serve as evidence that his father is bad at parenting partly because he never intended to have children in the first place.
It would also contribute to people viewing Mayor Jones as someone who makes poor decisions.
In "The Dragon's Secret" and "All Fear the Freak", Daphne's parents are shown to also harbor a strong dislike for Mayor Jones, not just towards Fred. In the latter episode, when Daphne and Fred reveal their engagement, Mrs. Blake makes it clear she blames Mayor Jones for this. From their perspective, their youngest daughter (who has shown interest in getting... something, in spite of age) wants to be with a boy who was the result of a fling by young and irresponsible couple, his father being completely inept at parenting and his mother regretting being associated with them to the point that she dumped the kid on the baby daddy, causing unnecessary drama. Who's the say history won't repeat?
Brad and Judy having Fred two years after they left Crystal Cove at the age when they could have been in college or possibly could have still been in high school sounds like something you'd hear in a movie about teens or young adults with miserable lives leaving their home to try to figure things out on their own, which makes this another play on the teen genre that Mystery Incorporated keeps poking at.
Mr. and Mrs. Blake don't like Mayor Jones, just as they don't like Fred. You'd think that because of Daphne's close friendship (and romance) with Fred, maybe the Blakes would want a connection with an influential family and try to influence Fred. Given some of Mayor Jones's political decisions like spending tax money on building a hit-or-miss tourist industry, it's possible they don't share the same ideas in politics. Mayor Jones is also shown to lean more on the antisocial side and doesn't seem to be as rich as the Blakes.
Assuming Crystal Cove is set in the same place where the real-life Crystal Cove State Park is, that places it in the city of Newport Beach in Orange County. Orange County is known as one of the most conservative counties in the country, yet is located between both liberal and conservative counties, putting it in mixed territory.
Of course Mayor Jones lets folks dress as monsters and run around doing illegal/morally suspect schemes for their own self-gain. It's something he's done himself.
Fred is seen as a bit of a control freak and oblivious as to how he makes other people feel. Given that Mayor Jones has been shown to be rather bossy and apathetic (not to mention being a failure of a supportive parent, especially if you consider Fred on the autism spectrum), it makes sense that Fred would act that way. Let's also not forget the name of his "father's" monster disguise.
The Gang are the only ones out of all the other mystery-solving groups that actively investigated monsters and unmasked them. The first Mystery Incorporated had no experience in this, which is part of why they're defeated by the Freak.
You'd think that the disappearance of the first Mystery Incorporated would've been more well known in Crystal Cove to the point that even twenty years later, someone would have recognized their signature locket and remember how there was a mystery-solving group before the recent one. For example, you'd think that someone like Sheriff Stone (who is said to have been in the police force for at least 27 years) would have said something. However, remember that Crystal Cove is full of Apathetic Citizens, and it should also be noted that it doesn't seem to be the kind of small town where everyone knows each other. In addition, it would seem that since the first Mystery Incorporated were more of a school club formed out of boredness and the fact that they didn't make as much of a name as their successors (ex. they didn't unmask monsters terrorizing the town; instead, they probably solved minor trivial mysteries) probably made their disappearance a forgettable headline. Not to mention that in this show, the present day takes place in an amalgam of the 1970's/2010's, so preserving the knowledge of missing persons from the 1950's might not have been as careful as it is in modern day.
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 Incorporated'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...
With the reveal of The Evil Entity corrupting everyone close to the gang, as well as their predescessors, Scrappy and Flim-Flam's presence in the spook museum. Considering Flim-Flam is a pre-teen con artist, while Scrappy is an over-achieving Boisterous Weakling, they'd probably give Mystery Inc. more to deal with besides the treasure. The Entity probably corrupted these two and ruined their relationship with the gang (and by extension their cousins) to keep them out of the way.
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?
Not only that, but families as wealthy as the Darrows and living in that era would surely have had live-in servants around the place; indeed, keeping up such a big mansion would've been impossible without some. Whatever became of them?
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 "The 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:
A common criticism towards the show is the characterization of the characters, especially the gang. Considering their world is a crapsack one, they're a product of their environment that will continue to cycle. And as the show reveals more of its plot, it turns out an Evil Entity has been influencing the events of the show this entire time. Previous mystery-solving groups have broken apart and failed because of their growing insanity from this Entity, and Daphne even explicitly wonders out loud after this revelation if any of them would even be friends without the Entity choosing them to be the chosen ones. This becomes ironic in the new universe when the gang are still friends with each other and with numerous other characters (and with better relations this time), most of the characters don't seem to have any mental problems in this world, and a common theory about the new universe is that Nova was the one who made it happen.
Mayor Jones is what would happen if a Scooby-Doo villain was ambitious enough and used very real strategies to get what they want, and get away with it for the next couple of decades. Do you really expect a Scooby-Doo villain in any other incarnation to blackmail our heroes — children — into incommunicado from their offscreen families, use chloroform to set up a Frame-Up, and kidnap a baby while threatening to hurt it? Not to mention the fact that, like every Scooby-Doo villain, he's the friendly stranger-turned-new-ally that the kids meet at the beginning of the episode, only to it to turn out that he was the villain-of-the-week... except the original Mystery Incorporated never gets to that part and it stays in 'friendly ally' territory for the new Mystery Incorporated for a long time until the Season 1 finale.
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.
It could also be that the woman in the magazine photo actually was someone he used to date, just not someone he'd ever been married to. It'd be easier to fake the appropriate emotions in front of Fred if that were the case, facilitating his pretense.
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.
Possibly the Nibiru Entity wasn't actually responsible for making all those criminals dress up like monsters; rather, it was responsible for them converging on Crystal Cove to do so. It concentrated a social phenomenon that was already happening.
In the alternate reality why is Fred's name still Fred. Since 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.
Problem is that Fred Jones implies it's a coincidence he and Fred share their first name. That "coincidence" part though does suggest that an outside force was involved in this happy 'accident'.
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
Perhaps he's got a workaround. Middle name, AKA, something of the sort.
The new universe more or less rebuilds itself to leave a suitable space for the gang. It's possible that it altered history enough that Brad Chiles was Brad Jones instead, by having one of Brad's ancestors change his name to match a stepfather's or something.
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.
Word of God implies that the new universe at the end is a Broad Strokes of the original canon, not the original canon straight-up.
Fred's fake mother. It is never explicitly stated that she was ever Mayor Jones's wife ("That's Fred's mom. She left when he was only a baby."), implying that Fred was born out of wedlock. Since this would therefore mean that Fred was probably unplanned, that puts into perspective why Mayor Jones is so neglectful of him; he didn't want or plan for a kid in the first place.
"All Fear the Freak" reveals that Mayor Jones was still in college when he forced the original Mystery Incorporated into exile, and it isn't indicated if he had graduated by the time Brad and Judy returned to Crystal Cove with Fred, so him having Fred edges very close to the possibility that he and his "ex" had Fred while in college or at the very beginning of their careers. Fred's mother could have left because she wanted to focus on her career over having a family while young.
Which then makes her Not So Different from Mayor Jones, since the both of them care greatly about their careers and didn't want a kid in the first place. But considering that Mayor Jones, for all his neglect of Fred, actually tried to be a good father while the mother of their child up and left early on and knowingly shifted the responsibilities of parenthood to someone who was in the same situation as her makes you wonder if she even wanted to put in any effort at all. This would also be an unsurprisingrevelation of his taste in romantic partners. On the other hand, it reflects how Fred's mother is a product of Mayor Jones's lies.
It's also implied in "The Shrieking Madness" that Mayor Jones was a charismatic and popular student in college and was involved in the party life, and you know what happens at college parties when two people get too tipsy...
Fridge Sadness: Why did Mayor Jones help out in the Krampus scheme, despite that he likely wouldn't receive anything in return (due to how bad his crimes were)? It isn't simply just a revenge plot against the original Mystery Incorporated or doing the right thing for once out of love for his son... Since the Season 1 finale showed that he still loved Fred and was heartbroken when he disowned & left him, wouldn't he be elated to hear that his 'son' wants his adoptive father's help to backstab his biological parents? As far as Jones can understand, his 'son' wants him back, or at least gives Jones one more time to instate a legacy via helping his 'son' finish what he could not; find the treasure and bask it all its glory.
At the end of "Pawn of Shadows", Angel reveals the truth and the episode ends with it having turned out the Freak had been watching the ending scene the whole time. It's a good thing that "All Fear the Freak" is implied to have happened later that night, or else who knows what he would have done to Angel if he had the time to deal with her.
The Freak blackmailed the original Mystery Incorporated into leaving their home or else he'd hurt their parents. Twenty years later, when the Freak gets arrested, they show no known intention to reunite with their family despite it now being safe to do so. What happened? Did they die? Moved away to start a clean slate and left nothing of their old life behind?