Nightmare in Red confirms that he truly did grow to love his son. He didn't show it usually because his good side was literally trapped in his subconscious. Through talking to said good side, Fred forgives him and acknowledges him as his the only true father he ever had.
Fred's almost narrow-minded obsession with traps and difficulty reading other people have led a few viewers to conclude he falls somewhere on the Autism spectrum.
Velma: Did she really love Shaggy or was he just the other guy to her, knowing that Daphne really liked Fred.
Badass Decay: Mr. E's actions never quite stop being threatening or competent, (with the exception of one instance of being Out-Gambitted) but you have to admit knowing he's grotesquely overweight and actually playing his background keytar music doesn't do a whole lot for his air of menace, and it gets particularly bad when he ends up being personally intimidated by a confrontational Shaggy at one point.
Scooby and Velma. Some sympathize more with Scooby than Velma in the "love triangle" with Shaggy, while some sympathize more with Velma. And some sympathize with neither of them because they both displayed creepy Yandere behaviour towards Shaggy.
Cargo Ship: Fred and traps. Seriously, he can't walk past a net or a cage without swooning over it.
Complete Monster: The Greater-Scope Villain, the Nibiru Entity, is a member of a normally benevolent inter-dimensional alien race called the Anunnaki; his own kind considers him the most evil member of their entire species. He's spent untold centuries corrupting and manipulating the people around him, especially the Team Pets of mystery solving teams, by perverting his species' ability to use animals as mediums to communicate, all working towards freeing him from his prison. In the process he's ruined and ended countless lives through his Unwitting Pawns (including Professor Pericles, who the Entity turned into a murderous psychopath) without a second thought. When he's finally released in the Series Finale, he proceeds to gleefully eat his loyal minions alive along with Mr. E. He follows this by turning Crystal Cove into Hell on Earth and devouring the entire town with sadistic glee, planning to move on to the rest of the universe when he's done, all for the sake of power. When Mystery Inc. finally kill him, erasing him from time in the process, we see what Crystal Cove would've been like without his influence: a normal town with everyone living good, happy lives, showing just how much pain and misery he was truly responsible for.
Continuity Lockout: As the show progresses and all the plot points and backstory are piled on about the questions about the Conquistadors and the original Mystery Incorporated, it becomes rather unfriendly to newer viewers regardless of the Previously On segments. The show's ending, however, at 52 episodes and 2 seasons, may mitigate this. It is nonetheless a lot better in one sitting.
Crazy Awesome: Just about all of the Monsters of the Week qualify to some degree, but Ernesto, Mary Ann Gleardon, Alice May, and Mrs. Wyatt really stand out.
Critical Research Failure: In the first episode, Angel Dynamite gives the call letters and frequency of her radio station, naming 101.4 on the AM dial. Two problems with this for anyone who has ever taken a look at a radio: AM stations are between 540 and 1610, in increments of 10 and no decimals (e.g. 760 AM, 1370 AM). In the US, FM stations, which do have decimals, only use odd numbers for the tenths place (e.g. 101.1, 101.3, 101.5 but never 101.4). Alternatively, this could be 555 applied to radio stations.
Evil is Cool: Professor Pericles is easily the most popular and memorable villain in the show.
Evil is Sexy: Alice May, especially as Obliteratix in episode 25.
Fan Nickname: As it turns out, Nibiru is not the name of the thing inside the sarcophagus seen with the cursed treasure. Nibiru is the name of a certain time when the thing's homeworld and Earth are able to interact with one another.
A lot of Mayor Jones' "wacky" moments from early in the season become this after seeing the finale...
"Mystery Solvers Club State Finals" is an amusing episode, and the reveal of Mudsy as the villain is rather funny. Season 2 then starts to imply that the animal or any unique companion to a Mystery solving group will turn evil because of the mystery of Nibiru.
Daphne's "radical idealist friend" Ernesto seems to be named after Ernesto "Che" Guevara.
"Hatecraft"'s ravenous follower Robert E. Howard is named after the author of the Conan the Barbarian novels, who really was a correspondent of Lovecraft's while he was in his twenties.
Growing the Beard: The first season, while starting strong, did struggle with balancing the mysteries, story arc, humor, and romance. As the first season progressed and romance mostly dropped, the show caught a better balance, using the characters to play off each other and develop, and focusing on the main Story Arc with goofy episodes in-between.
In "The Shrieking Madness", Shaggy reacts unfavorably to the vegan burgers being served. Funny because Casey Kasem insisted that Shaggy become a vegetarian in order to bring him more in line with Kasem's strict vegetarian diet.
When discussing plans for after High School, Fred implies that he and Shaggy will be rooming together, but actually asks if Shaggy prefers cotton or linen bedsheets.
When Scooby realizes that Shaggy's relationship with Velma is serious, he acts just like a jilted lover.
Scooby: Are you... cheating on me?
And when they're too caught up in a happy reunion to run from a Killer Robot dog, Velma tells them "Let's go, lovebirds."
Fred's dad's old fraternity Mu Gamma Tau only seem to be interested in working out and wrestling... a lot.
In episode 3, Rung Ladderton and Fred comment on each other's ascots... and then swap saying how good they look on each other.
In episode 4, Velma appreciatively looks Daphne over when Daphne changes into a bikini. Daphne then asks her to rub sunblock on her back.
Daphne gets some with Thorn of the Hex Girls in episode 7.
Thorn: I'm a good look for you, Daphne.
Episode 11 - Sheila Altoonian and Elizabeth Blake.
Episode 14 - The Principal and Angel Dynamite.
Episode 16 - When Aphrodite casts her love spell, everyone seems to fall for a member of the opposite sex...except Mayor Jones and Sheriff Stone, who are seen dancing together in the streets. Not to mention all the little dates they seem to go on...
Episode 20 - Velma and Amy the mermaid.
Episode 22 gives us Dr. Rick Spartan and his assistant Charles/Cachinga. They argue like an old married couple, but the minute Rick is seriously injured, Charles is rushing to his side, worried sick. Of course, Rick is married and his wife's love for him is the reason she dressed up like the Headless Horror to begin with, to try to convince him to live a normal, non-adventuring life, but it only plays down the Ho Yay a little.
By The Devouring, Marion has actually left Rick, presumably due to his adventuring lifestyle, but one can speculate.
Episode 24: Night Ranger collects magazines with men in what Daphne calls "mankinis."
In Season 2, we get one of the most blatantly intentional examples with Hot Dog Water and Velma, who have gone from rivals to partners and friends.... really, really close friends. Justified in that Velma now has a friend that can also understand her Techno Babble and enjoys science, where Velma is pretty much Marcy's first and only friend.
The altered credits in the episodes where Hot Dog replaced Daphne in the group show her hugging a picture of Velma!
Their final scene together in the Grand Finale makes it borderline canon.
The Hodag of Horror features a disgruntled Fred who complains about being labeled 'Scarf Boy' by Velma. If her codename of 'Smart Chick' is anything to go by, she chose all the codenames...including Daphne's codename of 'Smoking Hottie.'
Season 2 also gives us Ricky and Pericles' relationship. Pericles even seems to quite literally want Cassidy Williams to Die for Our Ship!
It doesn't help that by the time "The Devouring" happens Pericles has pretty much gone abusive boyfriend on Ricky, smacking him around and telling him he's only there to serve him.
Episode 45: Scooby and Shaggy go on an eating binge to chase away a gluttonous demon; they tuck into a giant cake at each end and end up kissing each other-on the lips!
Jerkass Woobie: Velma. You can't help but feel sorry for her when Shaggy picks Scooby over her. Granted, Shaggy probably wasn't a good match for her anyway...
Feel more sorry for her; she's all alone now that the gang's split up. Oh and remember...she's being blamed for it by Daphne.
Sheriff Stone can fall into this territory too, especially in "Dead Justice" and "All Fear the Freak".
Danny Darrow when he was a child; he and his family go crazy with greed after finding a piece of the planespheric disc, and their house sinks underground where he's forced to live out his life (about 75 years), obsessed over the piece, while he and his family grow old, and they all die. A run in with the original mystery inc. leads him to set traps all over the house, and he almost kills the current ones with them, and later with a fire poker. In one scene, the gang sets a trap, and Scooby lures him in while pretending to be his mother, he responds with a genuine hopeful smile and says "Mommy, you came back to me?" Despite knowing that she died years ago.
The members of the original Mystery Inc., with the possible exception of Professor Pericles, due to how the curse of Crystal Cove completely ruined their lives and warped them all into awful people.
Les Yay: The first season had open animosity between Velma and Hotdog Water. The stated reason was because they were simply scientific rivals, though many fans interpreted it as a Foe Yay situation. By season two the writers seem to have adopted this theory, or at least deliberately played with it. The most obvious sign is that, when Hotdog Water replaces Daphne briefly in the opening sequence, she's seen cuddling a photograph of Velma. To say nothing of her last appearance and line in the series: "That's my girl."
The current Mystery Incorporated is the latest in a long line of mystery-solving crews with a Talking Animal. Most of them have two men and two women. At least two of the people in each mystery solving gang end up together. We see pictures of them in the episode "Night Terrors." However, there's a group of monks, which could be easily dismissed since they're Catholic monks, but there's also a group of all girls. Make of that what you will...
Magnificent Bastard: Professor Pericles definitely qualifies — nearly every episode he shows up in, he gets exactly what he wants, usually at the expense of the gang. "The Wrath of Krampus" was the first time he's suffered a defeat. And that was because the entire town and Rouge Gallery were in on the Batman Gambit.
Moral Event Horizon: The Nibiru Entity gets one when, after it is freed, it proceeds to EAT Brad and Judy (AFTER they had pledged their servitude), then Mr. E., then the rest of the town, all for power (and you can tell it's enjoying it), and it claims it will go on to devour entire GALAXIES! Then again, it is the most evil Annunaki EVER. It's being the cause of corruption of all villains, even Professor Pericles, stands out too.
Narm / Narm Charm: Scooby ending his promise to get the gang back together and go after Pericles with "or my name isn't Scooby Dooby Doo!" either undercuts the tension entirely or just sort of works depending on who you are.
Nightmare Retardant: The Nibiru entity is terrifying for the most part, its initial appearance is.....not. Thankfully it doesn't stay in that form for very long, and its new look is a complete 180 in frightening.
Mayor Fred Jones Sr. was rescued twice. People hated him for being a Jerkass who put money ahead of his child's safety. The first time he was rescued he was revealed to be the Freak of Crystal Cove, the first season's Big Bad, meaning that one was supposed to dislike him, and he fell into Love to Hate as a truly nasty Knight of Cerebus, or if not then Hate Sink. He was rescued again when it was revealed that he's a better fit for a parent for Fred than his biological ones; Brad and Judy, whose greed exceeded the mayor's due to them being more closely connected to the curse. His best part's reconciliation with Fred and his later Cosmic Retconned self pulls him from being hated.
Romantic Plot Tumor: A general consensus for the first half of Season 1 was that too much time was spent on the relationship drama between the characters. It's considered to have gotten much better from Season 1's second half and onward.
While the show is considered very good by a lot of people, a very large amount of old school Scooby Doo fans hate it because of things like drastically changing or "derailing" old characters, ditching "Coolsville", focusing more on relationships than mysteries, and not having Scooby Snax (or at least not as prominently). The most passionate of haters even play the "ruin my childhood" card!
In a more specific example, the Hex Girls were hit with this considerably. While people love that Luna got her original skin-tone back and consider "Trap Of Love" one of the best parts of the cartoon, everything else is a Base Breaker. Their new designs received mixed reactions to the point where they later showed up in their traditional looks. Their music style was changed to a more contemporary style which made a lot of fans of their original songs disappointed at the newer versions of their songs, especially "Earth, Wind, Fire, and Air".
Unintentionally Sympathetic: Daphne's sisters losing their successful careers and marriages in the new timeline. It's supposed to be something of a Break the Haughty moment where those who succeeded at Daphne's expense were punished while she was rewarded, and Daphne's status as The Unfavorite is removed. Except, they didn't succeed at Daphne's expense, and her parents, who escape punishment, were the one's who held her in such little regard, and constantly reminded her of it. To make matters worse is that of her sisters, only Daisy was a Jerkass, three of them didn't show much personality (one of whom went unnamed), and her other sister, Delilah, was nicer to her than her own parents.
"The Creeping Creatures" involves a case with three gator-men trying to scare people away from their town. There are only three people around, all of them act super creepy, and just in case that wasn't enough, the shapes of their heads match the three gator-men. Are we even supposed to see a mystery in this?
"The Secret Serum" tries to fool the viewer into thinking Daphne's mother is the vampire attacking the town. The misdirection might have been more successful if she wasn't accompanied by a very obviously creepy, shifty-looking and pale assistant who's accompanied by creeping sound effects and walks without seemingly moving her feet.
In "Menace of the Manticore" it was painfully obvious that Hot Dog Water was the Manticore. And since they bring it up in season 2 it could also be a Late-Arrival Spoiler.
The entire point of "The Gathering Gloom"'s mystery. The rest of the gang chides Velma for immediately suspecting Count Evallo as the Monster of the Week, and begin investigating the incredibly friendly Oktoberfester blonde and her three beautiful daughters. Velma manages to find the evidence to prove Evallo's guilt, with the help of just Scooby and the Sheriff. To make things worse, while Velma was totally right, the Count, being a count, had diplomatic immunity.
In "The Song of Mystery", not only is Mary Anne is the only other character besides Luis, she's the only child that isn't affected by the song, and she's just the right height to be the monster!
Values Dissonance: Over a much shorter time period than most cases due to the timing. In the first half of season one, which premiered in 2010, Velma is shown as trying to force Shaggy to change his ways (eating less junk food, saying "like" less, changing his wardrobe) and overall coming off as manipulative with him. Back then, it was a funny series of jokes no one really took seriously, in or out of universe. A few years later, especially thanks to the rise of sites such as Tumblr, it's become a rather well-known and oft-discussed problem for men to manipulate their girlfriends (and debatably to a lesser extent, vice versa) in almost the exact same way Velma does to Shaggy, making the jokes now come off as a Double Standard. A similar, but less serious, case can be made for how Fred practically ignores Daphne even after they start dating.
The intention might have been to lead someone to trapped victims who needed medical help.
The whole gang still not having realized the gaping hole in Alice May's Daddy's Little Villain con by the time of her reappearance.
Season 2, Episode 9: While leaving fake evidence at Dougal McGuines' house was a somewhat smart move on Gary's part, leaving his own yearbook with his name in it and trying to frame a person that would give the gang evidence was not.
Brad and Judy aren't too bright. Their whole reasoning behind their Face–Heel Turn is to protect Fred from seeking the treasure and becoming corrupted. And thus the predictable outcome to this plan happens: THEY become corrupted and end up so obsessed with the treasure that they forget all about the son they were supposed to be protecting and willingly hurt him in order to get to the treasure.
In "The Man in the Mirror", Fred knows that his parents are searching for the Planispheric disk. So why, oh why, does he lead them directly to its hiding place at the abandoned factory instead of literally anywhere else?
What Do You Mean, It's for Kids?: This show is surprisingly darker, violent, gorier and scarier than the previous shows have (threats to kill the gang have occurred, stuff blows up, people get injured, etc.) yet it was rated TV-Y7-FV! Ironically, its sister show The Looney Tunes Show was rated TV-PG, yet is much tamer.
The Woobie: Fred. Fred. and Fred. Episode 26 revealed that he was taken away from his real parents by the mayor and he's leaving to find them. But deep down you can feel him sob and choke because all this time his real parents have been worried sick about him.
Don't forget Daphne. She was waiting to marry Fred but Fred has stated that the engagement is off and that Mystery Inc. is Dead. She's last seen crying that everything has just fell apart.
Fred gets it worse in the Season 2 premiere. Daphne's moved on, the plan failed, The Bad Guy Wins, oh, and he's been living as a hobo for a while now... someone give him a hug.