These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Lampshaded, averted and subverted in later seasonsnote (with the exception of X-Ray Johnny, where the "Books are knowledge, and knowledge is power" message is hammered in once a minute with no irony in sight; even Johnny Applesauce pales in comparison.).
Asspull: In "Johnny's 100th Episode" Mr. Mittens and Dark Vegan's reasons for wanting Johnny to come out of his coma come completely out of nowhere. At least Bling-Bling Boy has gotten along with Johnny occasionally.
Broken Base: The show does have its fans considering it's been going for six seasons due to having some actually good dialogue, parental bonuses, and admittedly some clever plot lines; but, due to overexposure from its respective networks, stagnant character development, way too much focus on Johnny (who many think to be unlikable), and poor animation in the later seasons, many have likewise taken a hating for it.
Cliché Storm: This show is criticized for rehashing a lot of stock cartoon plots, including its own.
Foe Yay: Bumper does this with Johnny a lot, whether Johnny is crossdressing or not; another example was in an episode where Johnny tries to change his personality in one of his sister's machines and, when he's stuck a smooth-talking British personality, Bumper implies to like this version of him a lot.
Gil is noticeably always excited to see Johnny; yet when he sees Johnny's sisters, he can't even remember their names.To make matters worse, in a episode is revealed that in his personal POV of the world, girls don't exist.
Mr. Black and Mr. White, whose Ho Yay is kind of blatant.
In the episode "Johnny McCool", at the end of the episode the twins are seen sighing at Gil eating a sandwich, then pans out to Gil sighing at Steve McCool, and it turns out it is a picnic. However the McCool presented is Dark Vegan in disguise.
Idiot Plot: There are a few episodes subjected to it here and there.
Iron Woobie: Dukey is pretty much this, still having his cheerful, lovable sense of humor despite being a Butt Monkey.
Johnny and Sissy look like siblings. Aside from that most likely unintentional instance, there's the writers' apparent fondness for Screw Yourself and everything related to it.
The scene after the beginning minutes of "Johnnyitis" in which Johnny, desperate to become sick in order to have an excuse to miss a big history test, eats a sick woman's used tissue. Said woman also had snot draining from her nose.
As of Season 5, Dukey now has the same voice actor as Johnny's dad, which proved an unpopular decision at best; the same goes for the change of Mary's voice actress.
Season 2 is this, but that's mostly due to some fans being put off by the shift in animation after Season 1; compared to Cyberchase and Caillou which had done similar but only after 4 seasons, this show at least had the common sense to switch early.
Though sadly by Season 5, the animation got even worse than before.
Susan and Mary Test are obviously the Dexters of the show, being redheaded genius children with a laboratory in their house.
Johnny is like Dee Dee, since both of them are Dumb Blonde annoyances who constantly cause trouble for their genius siblings.
Their parents are kind of like if one took Dexter's mom and dad and swapped their personalities, and then flanderized them: Johnny's Dad is a major neat-freak, while Dexter's Mom had her moments of this as well; Johnny's Mom is the head of the house and always working, while Dexter's Dad was just the head of the household.
Also, a female in the main cast is bothered by an Abhorrent Admirer, who is another nerdy genius child with their own laboratory; Bling-Bling Boy is the Mandark of the show.
Dukey can also be compared to Monkey, both being animals who have gained unusual abilities because of the genius children, Dukey's being talking, while Monkey becomes a superhero.
Let's not forget, there was also an episode of Dexter's Lab called "Dexter's Lab" in which Dexter finds a lost dog which he teaches to speak English.
Uncanny Valley: Speed McCool and Monkey; although that's probably intentional.
The Deranged Animation (starting in season two and getting worse from there) and bizarre, strangely exaggerated facial expressions (along with most characters' lack of pupils) are surprisingly unsettling; none of this is helped by the unappealing (or just plain ugly in some cases) character designs.
Dukey, who always seems to get frozen in a block of ice or turned to stone. Also, the episode "Bathtime for Johnny" where Johnny "forgot" his birthday and he sobbed his heart out for nearly the whole episode (see Tear Jerker above). Last but not least, most people go out of their way in the show to point out how ugly he is.